Progress 03/01/18 to 02/29/24
Outputs
Target Audience:The work from all objectives serves the academic community interested in agrobiodiversity generally, in crop genetic diversity, and the ways that past use and environment influence their diversity. It is also of interest to farmers utilizing landrace diversity in their cropping systems and those looking to increase diversity. Additionally, our work is important for the international NGO (research and outreach) community around the globe working with landraces, as well as government regulators and anyone interested in seed banking. Finally, our work is of interest to those working in pre-breeding of crops with adaptations to abiotic stress and those looking to understand the evolution of local adaptation in plants. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Our research activities provided training in molecular genetic techniques, greenhouse propagation, experimental design, data analysis, and pepper breeding for one postdoc, five graduate students, and two undergraduates this year. It also provided an opportunity to explore plant genetic resources and the implications of the international treaty on plant genetic resources on plant breeding and conservation. UNAM's postdoc led the writing and publishing of a paper in the Ecology and Evolution journal. An OSU student successfully defended a doctoral dissertation entitled, "Exploring the morphophysiology, ecology, and genotypic variation of drought adaptation and water deficit response in chile pepper (Capsicum spp.)", which used the collections made by this project and published an article in BMC Notes. Another OSU student successfully defended a MS thesis entitled, "Root phenotyping of chili pepper (Capsicum spp.) grown in rhizoboxes in well-watered and water deficit treatments", which also used accessions from this project. Moreover, an OSU undergraduate student completed her honors thesis on differences in seed morphology and seedling growth in wild, semiwild, and landrace pepper from Mexico using these accessions. One OSU graduate student from our team was successfully granted a USDA Predoctoral Fellowship to leverage our new collections to better understand the distribution of resistance to Phytophthora capsici root rot in landraces throughout Mexico and identify genetic variation within the chile genome associated with the disease phenotypes. This extends our work from abiotic to biotic stressors. We convened our research team for public, in-person meetings twice in this period: first for the 2023 Chile Convergence in Columbus, OH, in March 2023, and then for the the 2024 Chile Convergence (also in Columbus) in February 2024. In 2023, three OSU graduate students, two UNAM graduate students, and one UNAM postdoc presented on their ongoing research and future analyses at the convergence. In 2024, one UNAM graduate student, one UNAM postdoc, and three OSU graduate students presented (one of which had recently graduated and attended as a colleague given our continued collaboration). All co-PIs and technical staff attended to share knowledge, work on manuscripts, and make plans for our research team. Moreover, graduate students, postdocs, and undergraduates all presented their work at their universities: three OSU graduate students presented at OSU a total of four times, and the OSU undergraduate presented once. One UNAM postdoc gave a presentation to the UNAM postdoctoral community. The postdoc will be presenting at the Society for Molecular Biology and Evolution meeting in 2024, and an OSU graduate student plans to present on her work at a national conference in 2025. Chile Convergence 2024 Phenotyping for chili pepper (Capsicum sp.) under water deficit condition in rhizoboxes, Chee Ngui Changes in physiological state; environmental characteristics related to phenotypes, Jack McCoy Population genetic structure of landraces of chile pepper, Anayansi Sierralta Population genetic structure of chile pepper collections from the center of origin and diversity and its relationship with geographic and environmental factors, Natalia Martinez Identify and characterize loci involved in environmental adaptation (especially to drought), ascertain their putative function, and discern the geographic distribution of their alleles, Hannah Scheppler Chile Convergence 2023 An overview of response to water deficit in chile pepper (Capsicum sp.) and the influences of origin and domestication, Jack McCoy Whole genome sequencing: Haplotype studies for chili pepper (Capsicum sp.), Chee Ngui Identify and characterize loci involved in environmental adaptation, Hannah Scheppler Phenotypic response of wild and domesticated chile pepper to two temperature environments, Anayansi Sierralta Capturing the distribution as it shifts: chile pepper (Capsicum annuum L.) domestication gradient meets geography, Natalia Martinez Chile pepper genetic structure, Ana Laura Pérez Martínez How have the results been disseminated to communities of interest?We primarily disseminate our work through publication of our research results in peer reviewed journals, as well as through presentations at universities and professional conferences. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
AIM I: Mining our large collection of georeferenced Mexican accessions, we used genotyping-by-sequencing (GBS) to sequence 54 accessions for a total of 240 sequences from this project (82 wild, 64 semiwild, 177 landrace, 5 commercial). This added to the 191 previously sequenced (431 accessions in all). Sequenced accessions were densely sampled from southern and central Mexico, with less sampling in northern Mexico due to safety concerns. We have called single nucleotide polymorphisms (SNPs), filtered for read depth, minimum allele frequency and missing data per SNP, resulting in >150K SNPs. Thus, we finalized a robust genetic dataset from which to address objectives within both AIM I and AIM II. Our current analyses of population genetic structure of our Mexican collections using fastStructure show that wild, semiwild, landrace, and commercial types of chile peppers are genetically differentiated. However, we also see genetic variation within groupings, especially within landraces. Leveraging the chile pepper geographic distributions from AIM III, we mapped the genetic clusters assignments from fastStructure and found geography also organizes chile pepper variation. Wilds, semiwilds, and landraces from a given region show similar assignments, meaning that different types from the same region are more genetically related than they are to their same type in other regions. Moreover, domestication groupings showed isolation by distance (IBD), with accessions from geographically close locations more likely to show genetic similarity (i.e., to share alleles) than those from more distant locations. Nonetheless, environment also structures genetic variation in peppers in Mexico. We found evidence of isolation by environment (IBE) within groupings. Cultivated accessions collected from similar environments (based on, e.g., mean diurnal range, temperature seasonality, precipitation of the warmest quarter) more likely to share alleles. This may indicate that farmers in similar environments preferentially share seed, perhaps benefiting from better adaptation. Wild accessions collected from the forest showed more IBD than IBE (except with temperature seasonality). This points to natural seed dispersal, rather than adaptive human-mediated dispersal. We will quantify the presence and magnitude of gene flow among our types to better understand the dynamics shaping their genetic backgrounds and potential sources of adaptive variation. We plan to submit a manuscript on overall population structure analysis (Martinez-Ainsworth et al. in preparation), as well as one using a subset of our collections (Perez-Martinez et al. in preparation). We published a manuscript on population structure across diverse Capsicum species. We sequenced a global collection of 467 accessions representing eight species, from highly domesticated to wild, using 22,916 SNP markers across the twelve chromosomes.We found these species varied in levels of genetic diversity and differed in the size of genetic bottlenecks experienced. We found that levels of diversity negatively correlated to levels of domestication, with the more diverse being the least domesticated. The GBS sequence of the global collection was made publicly available on the NCBI short read archive under the project name PRJNA876725 and SNP datasets were made available on zenodo at https://doi.org/10.5281/zenodo.7268809. AIM II: We used the same SNP data from AIM I to clarify regions of the chile pepper genome that appear to have undergone selection from environmental and soil factors. First, we explored overall genetic relatedness among our accessions using principal component analysis (PCA). For our genome-wide association (GWA), we use a mixed model to predict the GBS data from PCA output (PC1 and PC2), the environmental variables (i.e., phenotypes), and other covariates, such as latitude, and using a proxy for false discovery rate called q-value. This GWA is also called an environmental association analysis (EAA) or a genotype-environment association (GEA). Our current analyses identify several chile pepper chromosomes that may contain loci associated with environmental parameters. We are still optimizing the models, but there are clear p-value outliers throughout the genome, with high peaks (i.e., strong associations) for variables such as precipitation of the driest and warmest parts of the year (on chromosomes 1, 9, and 12), soil pH (on chromosomes 1 and 12) and isothermality (on chromosome 6). Since we expect to identify a large number of loci of interest, we will combine our GWA with outlier analyses that identify loci that are likely to have experienced selection, such as Fst and spatial ancestry analysis (SPA), as in Bernau et al. (2023). By combining methods, we will narrow down the list of putative candidate loci to those that are most promising for future investigation. Apart from this overall analysis, we plan to perform sub-analyses for wild and landrace types, to see if types differ in the strength of genetic associations with environmental variables or in the important variables. Wilds may be experiencing more intense selection from the environment; landraces may have fewer associations with precipitation due to management, such as irrigation. Finally, we will map the geographic distribution of alleles at those loci, thereby illuminating the distribution of adaptive genetic variation across the landscape. We will prepare a manuscript (or two) on this work (Scheppler et al. in preparation). This new analysis builds on our Oaxaca-only EAA (Bernau et al. 2023), where we found fifteen priority loci whose genetic variation covaried with environmental variation and were also allele frequency outliers (i.e., Fst and/or SPA). Many of the priority loci were further validated with phenotypic response to water deficit and neighboring haplotype blocks harbor genes with abiotic stress-related functions. We are eager to assess the overlap between loci identified by Bernau et al. (2023) with those currently being revealed. Finally, to inquire into the genes surrounding loci of interest from Bernau et al. (2023), as well of those we are uncovering now, we resequenced ten accessions with higher coverage genotyping. We have called SNPs (~10 to 70 million SNPs per genome) and are filtering those SNPs for quality. We will be assessing patterns of genetic variation within the haplotype blocks of interest at relevant annotated genes. AIM III: We published a manuscript on the range of environments inhabited by, and geographic distribution of, Mexican peppers from along a domestication gradient: wild, semiwild, landrace, and commercial (Martínez-Ainsworth et al. 2023). Using GPS coordinates from each accession and corresponding climatic data (e.g., bioclim variables), we created maps using MaxEnt modeling and extracted environmental parameters from those distributions. We used these data to (1) discern the environmental factors that climatically differentiate the pepper types and (2) compare projected geographic distributions along the domestication gradient under current climatic conditions, as well as under climate change scenarios. We identified a contraction, followed by an expansion, of the environmental niche and geographic distribution as domestication proceeded, indicative of human modification of the niche. We predict that future climate change scenarios will more severely impact natural populations than other domestication categories, most likely because they lack buffering from human management. Moreover, we showed that contact areas between wild and cultivated types may decrease, which could disrupt the evolution of cultivated diversity. Finally, this work also gives us insight into the location of environmental extremes where accessions of each type may potentially possess physiological adaptations of interest.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Mart�nez-Ainsworth, N., Scheppler, H., Moreno-Letelier, A., Bernau, V., Kantar, Mercer, K. L., & Jard�n-Barbolla, L. (2023). Fluctuation of ecological niches and geographic range shifts along chile peppers domestication gradient. Ecology and Evolution 13 (11), https://doi.org/10.1002/ece3.10731
Occurrence points by domestication category, the complete ODMAP protocol report, and R-markdown code for all analyses herein included are available at the following Dryad link: https://doi.org/10.5061/dryad.c2fqz61d9
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Bernau, V.M*., Kantar, M., Jard�n Barbolla, L. McCoy, J.E.*, Mercer K.L., and McHale, L. 2023. Genomic signatures of adaptation to abiotic stress from a geographically diverse collection of chile peppers (Capsicum spp.) from Mexico. bioRxiv. https://doi.org/10.1101/2023.08.13.553093
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2024
Citation:
Mart�nez-Ainsworth, N., Scheppler, H., Moreno-Letelier, A., Bernau, V., Kantar, Mercer, K. L., & Jard�n-Barbolla, L. Domestication gradient in Capsicum annuum chile peppers center of origin: implications under climate change scenarios drawn from niche models and genomic diversity. accepted for the Annual Meeting of the Society for Molecular Biology and Evolution (SMBE), taking place July 7-11, 2024 in Puerto Vallarta, M�xico.
- Type:
Book Chapters
Status:
Accepted
Year Published:
2024
Citation:
Mart�nez-Ainsworth, N., Mercer, K. L., Sierralta-Guti�rrez, A., P�rez-Mart�nez, A. L., Mancilla-Gayt�n, V. A. & Jard�n-Barbolla, L. (tba). Evolution under domestication: genes, organism and management intersection in Mexican chiles. Book chapter in Biodiversity, management and domestication in the Neotropics. Casas, A., Peroni, N., Parra, F., Lema,V.S., Aguirre-Dugua, X., Ar�valo-Mar�n, E., Alvarado-Sizzo, H., Blancas, J. (Editors). Springer Nature.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
McCoy, J, Mart�nez, N, Bernau, V, Scheppler, H, Hedblom, G, Adhakari, A, McCormick, A, Kantar, MB, Jard�n-Barbolla, L, McHale, L, Mercer, K, Baumler, D. 2023. Population structure in diverse pepper (Capsicum spp.) accessions. BMC Res Notes 16, 20 https://doi.org/10.1186/s13104-023-06293-3
The GBS sequence of this collection was made publicly available on the NCBI short read archive under the project name PRJNA876725 and SNP datasets were made available on zenodo at: https://doi.org/10.5281/zenodo.7268809
|
Progress 03/01/22 to 02/28/23
Outputs
Target Audience:The work from all objectives serves the academic community interested agrobiodiversity generally, genetic diversity in crops, and the ways that past use and environment influence their diversity. Farmers utilizing landrace diversity in their cropping systems and those looking to increase diversity would also be interested. Additionally, our work is also of interest to the international NGO and research institute community around the globe working with landraces, as well as regulators and other interested parties. Finally, our work is of interest to those working in pre-breeding of crops with adaptations to abiotic stress and those looking to understand the evolution of local adaptation in plants. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Our research activities provided training in molecular genetic techniques, greenhouse propagation, crossing, experimental design, data analysis, and pepper breeding. It provided an opportunity to explore plant genetic resources and the implications of the international treaty on plant genetic resources on plant breeding and conservation. One of the UNAM's students led the writing of the article already published in the American Journal of Botany. The postdoc at UNAM led the writing of a paper on the change in the ecological niche associated to the domestication process. An OSU graduate student published two papers: one on phenotypes of water deficit tolerance in PLOS ONE and another on genetic structure of the global collection. OSU graduate students made presentations within the university on their research, one presented at a national meeting, and one submitted a proposal to USDA for a Predoctoral Fellowship building on the work with these collections. An undergraduate student at OSU worked on her honors thesis research on the effects of domestication on seed and seedling characteristics in pepper from across an environmental gradient. Finally, a postdoc at UNAM and a graduate student at OSU worked with the PIs on a new proposal to the AFRI Physiology of Agricultural Plants panel building on this work to clarify thefunctional genetic dimensions of climate adaptation in Capsicum. How have the results been disseminated to communities of interest?We primarily disseminate our work through publication of our research results in peer reviewed journals, as well as through professional conferences. What do you plan to do during the next reporting period to accomplish the goals?Regarding AIM I, we will genotype by sequencing one more set of 94 pepper accessions to include in our analyses. This way, we will have data from 282 accessions sequenced under this project, as well as further 94 accessions collected under this project but sequenced thanks to an UNAM collaboration. Finally, we will sequence data from the 180 accessions collected in southern Mexico previously (Taitano et al. 2019). In total we will have more than 550 accessions sequenced. We will then filter, call and map SNPs from all accessions and begin the analysis of population genetic structure of our full slate of Mexican collections and will compare that to the global collection. We will prepare at least one manuscript from this analysis. We plan to also publish the paper on the GBS analysis of population structure of previous collections currently underway (Perez-Martinez et al.). For AIM II, we will begin to use the SNP data generated in AIM I to run initial demographic models, which will allow us to begin assessing the chile pepper genome for regions that appear to have undergone selection. We will also initiate an environmental association analysis on our Mexico-wide collection looking at wild and cultivated materials separately and together. Relatedly, we will submit our Oaxaca-only environmental association analysis manuscript after further clarifying the genes inherited together within loci of interest. We look forward to assessing the overlap between loci identified in the analysis of a geographically restricted set of accessions (Oaxaca-only) with those collected from across Mexico. Finally, we will resequence a subset of accessions with higher coverage to have a better sense of the genome surrounding loci of interest. For AIM III, we will finalize our geographic analyses and submit our manuscript. We will also use our data to identify a suite of accessions to prioritize for virus/viroid testing and exportation from Mexico based on the extreme nature of their environments of origin for future research. Finally, we will meet twice as a research team: once in Ohio and once at an international meeting to help us collaborate on ongoing work and grant proposals and present our research to a broader community. We aim to resubmit our new AFRI proposal in August.
Impacts
What was accomplished under these goals?
AIM I: Determine the population genetic structure of chile pepper collections from the center of origin and diversity and its relationship with geographic and environmental factors During the 2022-2023 year, students grew seedlings and performed DNA extractions. We had sequenced 94 collections prior to the pandemic (mostly wild or semiwild types) and sent 94 more individual accessions, mostly Capsicum landraces, for sequencing at the end of 2021. In December 2022, we sent the third plate for sequencing, which was made up of 94 accessions, including four wild, 13 arvense, 75 landrace and one commercial accession. Data from all three plates are now available for analysis. We plan to sequence one more plate of pepper DNA (currently being extracted in Mexico and Ohio) to fill out the diversity of the sequenced collections. This fourth and last plate will comprise approximately 50 wild, 30 arvense and 14 landrace accessions. We are actively preparing the data for analysis by calling SNPs and designing analysis pipelines for our population genetic analyses. In addition, we analyzed two other datasets related to our investigations. First, using SSR data from the Oaxaca portion of our collection from genotyping done outside the scope of this grant, we assessed population structure and submitted and published a manuscript in the American Journal of Botany. We found strong genetic differentiation between highland and lowland chile landraces. Moreover, our evidence suggests that gene flow is facilitated by the management of landraces and semiwild plants in backyards. One last finding of this paper is that the genetic affinity of one of the Tehuantepec Isthmus (Oaxaca) landraces with highlands may be explained by the social history of the indigenous peoples in the zone. Second, using genotyping by sequencing (GBS) data acquired from one of our co-PIs from 467 landraces of four species of pepper collected and sourced from seed sellers from across the globe, we published a manuscript exploring the genetic structure. By comparing species, we were able to discover that levels of genetic diversity negatively correlate to levels of domestication, with the more diverse species being the least domesticated. Further, we plan to leverage data from this global collection to better understand our extensive recent collections in Mexico funded on this grant. In particular, we plan to further compare their genetic structures. In the next couple of months, we plan to submit a manuscript exploring the effect of management regimes on genetic structure based on the analysis of 119 accessions for which we already have both GBS and passport data regarding the management system from which they were collected. Our preliminary results indicate that backyard systems have greater levels of gene flow with the nearby rainforest wild populations, in contrast monoculture populations have very low level of genetic exchange with wild and semiwild populations. The GBS sequence of the global collection was be made publicly available on the NCBI short read archive under the project name PRJNA876725 and SNP datasets were made available on zenodo at https://doi.org/10.5281/zenodo.7268809 AIM II: Identify and characterize loci involved in environmental adaptation (especially to drought), ascertain their putative function, and discern the geographic distribution of their alleles We are awaiting DNA sequence data from AIM I to perform the analyses related to AIM II. However, now that we have three plates of DNA, we have begun to call SNPs and figure out our analysis pipeline. However, we made related progress on data from a subset of our collection from the Mexican state of Oaxaca, which had already been sequenced (Taitano et al. 2019). We worked with this Oaxaca data to clarify loci involved in adaptation to abiotic stress in two ways: First, we progressed on the manuscript detailing our previously performed environmental association analysis (EAA) to identify potentially adaptive loci for extreme environments. We had previously made associations between genetic variation and environmental variation associated with the locations of origin of the pepper lines. Multiple loci had been found to be associated with precipitation variables, which may mean that they may be relevant to drought tolerance. We then looked at annotations of the pepper and other genomes to investigate the identity and putative function of genes present in the loci of interest. We expect this manuscript to be submitted in the next couple of months. We also leveraged our knowledge of these loci of interest to more deeply resequence a set of 10 pepper accessions, some of which we suspect to harbor alleles for abiotic stress tolerance. We hope to get this data in June 2023 and we look forward to working with it in the coming year. We hope to better understand sequence variation in all loci of interest identified from the EAA (above) and that will be identified from AIM II. AIM III: Discern the geographic distribution and environmental envelope of wild, semiwild, landrace, and commercial accessions of chile from across Mexico and explore how climate change will affect their future potential distribution. We performed analyses and wrote a manuscript to better understand the range of environments and geographic distribution of Mexican peppers from along a domestication gradient: wild, semiwild, landrace, and commercial. We had collected GPS coordinates on each collected accession, which allowed us to utilize corresponding climatic data (e.g., bioclim variables) to track the environmental space from which we were sampling. We were able to create maps using MaxEnt modeling to visualize the geographic distribution of peppers niche from along this domestication gradient. Then we extracted environmental parameters from those distributions to clarify the environmental space utilized by these different pepper types. We have used this data to (1) Discern the environmental factors that climatically differentiate the pepper types and (2) Compare projected geographic distributions along the domestication gradient under current climatic conditions, as well as under multiple near-future climate change scenarios. We identified a contraction followed by an expansion of the environmental niche and geographic distribution along the domestication gradient, indicative of human modification of the niche. We also observed that under future climate change scenarios we predict a more severe impact on natural populations than other domestication categories, most likely because they lack the buffering effect derived from human management. Moreover, the contact areas between wild and cultivated types may decrease, which could potentially disrupt the evolution of cultivated diversity. Finally, this work also gives us insight into the location of environmental extremes where accessions of each type may potentially possess physiological traits of interest to withstand such extremes. The manuscript was submitted to bioRxiv during this year, but will be submitted to Ecology and Evolution next year.
Publications
- Type:
Journal Articles
Status:
Submitted
Year Published:
2023
Citation:
Mart�nez-Ainsworth, N.E., H. Scheppler, A. Moreno-Letelier, V. Bernau, M.B. Kantar, K.L. Mercer, and L. Jard�n-Barbolla. Capturing the distribution as it shifts: chile pepper (Capsicum annuum L.) domestication gradient meets geography. bioRxiv. In revision for Ecology and Evolution.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
McCoy, J., N. Mart�nez-Ainsworth, V. Bernau, H. Scheppler, G. Hedblom, A. Adhikari, A. McCormick, M. Kantar, L. McHale, L. Jard�n-Barbolla, K.L. Mercer, and D. Baumler. 2023. Population structure in diverse pepper (Capsicum spp.) accessions. BMC Research Notes, 16(1), 1-7. https://doi.org/10.1186/s13104-023-06293-3
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
McCoy JE, McHale LK, Kantar M, Jard�n-Barbolla L, Mercer KL (2022) Environment of origin and domestication affect morphological, physiological, and agronomic response to water deficit in chile pepper (Capsicum sp.). PLOS ONE 17(6): e0260684. https://doi.org/10.1371/journal.pone.0260684
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
P�rez-Mart�nez A. L., Eguiarte L. E., Mercer K. L., Mart�nez-Ainsworth N. E., McHale L., van der Knaap E, and Jard�n-Barbolla L (2022) Genetic diversity, gene flow and differentiation among of wild, semiwild and landrace chile peppers (Capsicum annuum L.) populations in Oaxaca, Mexico American Journal of Botany, https://doi.org/10.1002/ajb2.16019
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Khoury, C., S. Brush, D. Costich, H. Curry, S. de Haan, J. Engels, L. Guarino, S. Hoban, K. Mercer, A. Miller, G. Nabhan, H. Perales, C. Richards, C. Riggins, I. Thormann. 2022. Crop genetic erosion: understanding and responding to loss of crop diversity. New Phytologist 233:84118 doi.org/10.1111/nph.17733
|
Progress 03/01/21 to 02/28/22
Outputs
Target Audience:The work from all objectives serves the academic community interested agrobiodiversity generally, genetic diversity in crops, and the ways that past use and environment influence their diversity. Farmers utilizing landrace diversity in their cropping systems and those looking to increase diversity would also be interested. Additionally, our work is also of interest to the international NGO and research institute community around the globe working with landraces, as well as regulators and other interested parties. Finally, our work is of interest to those working in pre-breeding of crops with particular adaptations to abiotic stress and those looking to understand the evolution of local adaptation in plants. Changes/Problems:Our original AIM III has been constrained due to restrictions on our ability to import chile pepper seeds from Mexico to the US from APHIS regulations that went into effect after we received this grant. See these links for announcements on new testing for viroids and a virus, respectively, that pepper seeds can carry: https://www.aphis.usda.gov/import_export/plants/plant_imports/federal_order/downloads/2019/DA-2019-21.pdf https://www.aphis.usda.gov/import_export/plants/plant_imports/federal_order/downloads/2019/DA-2019-28.pdf Due to these regulations, we now need an official and extended phytosanitary test of the seed in Mexico before exporting. During the 2021-2022 year, we finally were able to work with Mexican phytosanitary authorities to administer the test needed on seeds we required for our Within Mexico crosses, so we could import the seeds with the appropriate phytosanitary documentation. The testing is costly, so were only able to test and send six of the thousands of accessions we collected and had hoped to share between institutions. We continue to create F4:5 RILs to carry out the original work of AIM III. However, due to delays imposed by the covid pandemic, as well as these enhanced restrictions on seed importation, we will not be able to complete the water deficit experiments and analyses for the QTL mapping using the populations. Instead, we will complete a new aim that utilizes the extensive germplasm collections we made throughout Mexico in AIM I to better understand the current geographic distribution of this genetic resource and its predicted response to climate change. In particular, these analyses bring to bear our georeferenced collections to create the best understanding to date of the distribution of pepper accessions from across the domestication gradient. It also helps us identify accessions that push the boundaries of the environmental conditions inhabited by peppers--accessions that might be quite interesting for further study of their abiotic stress tolerances. (New) AIM III: Discern the geographic distribution and environmental envelope of wild, semiwild, landrace, and commercial accessions of chile from across Mexico and explore how climate change will affect their future potential distribution. We have described the progress we have made on this new AIM III in the Accomplishments section, as well as how we expect to progress on this work in our next reporting period. What opportunities for training and professional development has the project provided?Our research activities provided training in molecular genetic techniques, greenhouse propagation, crossing, experimental design, data analysis, and pepper breeding. It provided an opportunity to explore plant genetic resources and the implications of the international treaty on plant genetic resources on plant breeding and conservation. The postdoc at UNAM presented a poster (and an OSU graduate student coauthored it) at an academic meeting on the ecogeographic nature of pepper's domestication gradient. Another OSU graduate student made a presentation within the university on growth and physiological responses to water deficit. An undergraduate student at OSU completed her honors thesis on differences in root growth and physiology traits in pepper from across an environmental gradient. How have the results been disseminated to communities of interest?We primarily disseminate our work through publication of our research results in peer reviewed journals, as well as through professional conferences. What do you plan to do during the next reporting period to accomplish the goals?Regarding AIM I, we will filter, call and mapping SNPs in GBS datasets from our collections. We will also genotype by sequencing two more sets of 94 pepper accessions to include in our analyses. We then plan to begin the analysis of population genetic structure of our full slate of Mexican collections and will compare that to the global collection. We plan to publish our paper on the SSR analysis of population structure (Perez-Martinez et al.), as well as submit our manuscript on population structure analysis from the global collection. For AIM II, we will begin to use the SNP data generated in AIM I to run initial demographic models, which will allow us to begin assessing the chile pepper genome for regions that appear to have undergone selection. We will also initiate an environmental association analysis on our Mexico-wide collection looking at wild and cultivated materials separately and together. Relatedly, we will submit our Oaxaca-only environmental association analysis manuscript after further clarifying the genes inherited together within loci of interest. We look forward to assessing the overlap between loci identified in the analysis of a geographically restricted set of accessions (Oaxaca-only) with those collected from across Mexico. Finally, we will resequence a subset of accessions with higher coverage to have a better sense of the genome surrounding loci of interest. For (original) AIM III, we will continue the process of creating F4:5 populations from our US x Mexico and Within Mexico crosses. For (new) AIM III, we will finalize our geographic analyses and submit our manuscript. We will also use our data to identify a suite of accessions to prioritize for virus/viroid testing and exportation from Mexico based on the extreme nature of their environments of origin.
Impacts
What was accomplished under these goals?
During this past year (3/2021-2/2022), the global COVID-19 pandemic continued. While much activity resumed in our US institutions, our Mexican colleagues continued to face challenges. Despite much progress on our research, we have decided to adjust our third aim (see Project Modifications). Here, we will discuss what we did for our original AIMS and also our new AIM III. AIM I: Determine the population genetic structure of chile pepper collections from the center of origin and diversity and its relationship with geographic and environmental factors Covid slowed this aim in multiple ways. First, it reduced access of our Mexican colleagues to their lab where seedlings could be grown and DNA extracted. During the 2021-2022 year, students grew seedlings in their homes and ran batches of DNA extractions when they were granted rotating lab access (to reduce densities). Having already sequenced 94 collections prior to the pandemic (mostly wild or semiwild types), we were able to send 94 more individual accessions, mostly Capsicum landraces, for sequencing at the end of 2021. Because of covid delays at the University of Minnesota Genomics Center (UMGC), the data set took five months to be processed; we are currently actively preparing it for analysis. In addition, we analyzed two other datasets related to our investigations. First, using SSR data from the Oaxaca portion of our collection from genotyping done outside the scope of this grant, we assessed population structure and prepared a manuscript that we submitted to the American Journal of Botany. In particular, we found strong genetic differentiation between highland and lowland chile landraces. Moreover, our evidence suggests that gene flow is facilitated by the management of landraces and semiwild plants in backyards. One last finding of this paper is that the genetic affinity of one of the Tehuantepec Isthmus (Oaxaca) landraces with highlands may be explained by the social history of the indigenous peoples in the zone. Second, using genotyping by sequencing (GBS) data acquired from one of our co-PIs from 467 landraces of four species of pepper collected and sourced from seed sellers from across the globe. A manuscript exploring the genetic structure of these 467 individuals was invited to a special issue in Frontiers in Genetics. Further, we plan to leverage this data to better help us understand our extensive recent collections in Mexico funded on this grant by comparing their genetic structures. The GBS sequence of global collection will be made publicly available. AIM II: Identify and characterize loci involved in environmental adaptation (especially to drought), ascertain their putative function, and discern the geographic distribution of their alleles Since we did not yet have DNA sequence data from AIM I to use for analyses of our overall collection, we worked with data from a subset of our collection from Oaxaca, which had already been sequenced (Taitano et al. 2019). We worked with this data to clarify loci involved in adaptation to abiotic stress in two ways: First, we progressed on the manuscript detailing our previously performed environmental association analysis (EAA) to identify potentially adaptive loci for extreme environments. We had previously made associations between genetic variation and environmental variation associated with the locations of origin of the pepper lines. Multiple loci had been found to be associated with precipitation variables, which may mean that they may be relevant to drought tolerance. We then looked at annotations of the pepper and other genomes to investigate the identity and putative function of genes present in the loci of interest. We also leveraged our knowledge of these loci of interest to find funds to more deeply resequence a set of 10 pepper accessions (many of which are potential parents of populations being created for Aim III). While the groundwork has been laid for this project (accessions chosen, methods determined, seedlings grown), we look forward to working with the data in the coming year. These resources will help us better understand the genomic context for the loci of interest we identify with this grant. (Original) Aim III: Locate quantitative trait loci (QTL) affecting phenology, physiology, and agronomic performance under drought in the greenhouse (GH) in Mexican and US materials Within Mexico crosses: Due to import/export restrictions, we focused on exporting from Mexico to Ohio and Hawaii only a few collected pepper accessions from very dry and very wet environments needed for AIM III. These accessions are currently undergoing population development at UHI alongside similar crosses whose parents were sourced previously from the more limited collection at OSU. This work is very delayed in comparison to our original plans. Specifically, there are currently three populations are that are being advanced: (1) Ca0692 xCa0718 - with maturing F1 plants, (2) Ca0087x Ca0310 - with 164 F2 individuals, (3) Ca0129 x Ca0310 - with 74 F2 individuals. US x Mexico crosses: Having initiated 37 crosses, we used experimental evidence from McCoy et al. (2022) to identify favored parental pairings between Mexican and US parents. As a result, we have been emphasizing our favorite four populations for further development. Though these populations are progressing, greenhouse damage and miscommunications with greenhouse staff led to the loss of several lines, requiring us to return to earlier generations to further build up populations. We have been working specifically with the following populations: (1) Ca0344 x Canoncito - with 103 individuals at the F3, (2) Ca0045 x PI631153 - with 26 F3 individuals and 98 F2 individuals, (3) Ca0045 x PI 592822 - with 103 F3 individuals. Populations from US x Mexico and Within Mexico crosses need to be advanced to the F4:5 generation and increased to a population size of 144 individuals. Finalizing these populations and performing the subsequent GH can no longer be completed within the scope of this grant. (New) AIM III: Discern the geographic distribution and environmental envelope of wild, semiwild, landrace, and commercial accessions of chile from across Mexico and explore how climate change will affect their future potential distribution. We were able to use our time isolated from our labs to better understand the range of environments and geographic distribution of Mexican peppers from along a domestication gradient: wild, semiwild, landrace, and commercial. We had collected GPS coordinates on each collected accession, which allowed us to utilize corresponding climatic data (e.g., bioclim variables) to track the environmental space from which we were sampling. We were able to create maps using MaxEnt modeling to visualize the geographic distribution of peppers from along this domestication gradient. Then we extracted environmental parameters from those distributions to clarify the environmental space utilized by these different pepper types. We have used this data to (1) Discern the environmental factors that climatically differentiate the pepper types and (2) Compare projected geographic distributions along the domestication gradient under current climatic conditions, as well as under multiple near-future climate change scenarios. We identified an expansion of the environmental niche and geographic distribution along the domestication gradient, indicative of human modification of the niche. We also observed that that predicted climate change will be impact natural populations more severely since they lack the buffering effect derived from human management. Moreover, the contact areas between wild and cultivated types may decrease, which could potentially disrupt the evolution of cultivated diversity. Finally, this work also gives us insight into the environmental extremes where accessions of each type may be potentially found to possess physiological traits of interest.
Publications
- Type:
Journal Articles
Status:
Under Review
Year Published:
2022
Citation:
McCoy JE, McHale LK, Kantar M, Jardón-Barbolla L, Mercer KL (2022) Environment of origin and domestication affect morphological, physiological, and agronomic response to water deficit in chile pepper (Capsicum sp.). PLOS ONE 17(6): e0260684. https://doi.org/10.1371/journal.pone.0260684
- Type:
Journal Articles
Status:
Under Review
Year Published:
2022
Citation:
Pérez-Martínez A. L., Eguiarte L. E., Mercer K. L., Martínez-Ainsworth N. E., McHale L., van der Knaap E, and Jardón-Barbolla L (2022) ⿿Genetic diversity, gene flow and differentiation among of wild, semiwild and landrace chile peppers (Capsicum annuum L.) populations in Oaxaca, Mexico American Journal of Botany, https://doi.org/10.1002/ajb2.16019
|
Progress 03/01/20 to 02/28/21
Outputs
Target Audience:The work from all objectives serves the academic community interested agrobiodiversity generally, genetic diversity in crops, and the ways that past use and environment influence their diversity. Farmers utilizing landrace diversity in their cropping systems and those looking to increase diversity would also be interested. Additionally, our work is also of interest to the international NGO and research institute community around the globe working with landraces, as well as regulators and other interested parties. Finally, our work is of interest to those working in pre-breeding of crops with particular adaptations to abiotic stress and those looking to understand the evolution of local adaptation in plants Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Our research activities provided training in field collection of crop genetic resources, including appropriate interactions with Mexican farmers and community members. Training was also received in molecular genetic techniques, greenhouse propagation, crossing, experimental design, data analysis, and pepper breeding. It provided an opportunity to explore plant genetic resources and the implications of the international treaty on plant genetic resource on plant breeding and conservation. An OSU graduate student was able to attend an academic meeting and made presentations within the university on phenotypic responses to water deficit. Students at the UHI presented on the efficacy of crossing within divergent populations and on the population structure of global landrace collection. How have the results been disseminated to communities of interest?We primarily disseminate our work through publication of our research results in peer reviewed journals, as well as through professional conferences. What do you plan to do during the next reporting period to accomplish the goals?Regarding AIM I, we will continue to extract DNA and perform genotyping by sequencing on wild and landrace collections from throughout Mexico, hopefully by the end of 2021. Once that is complete, we plan to begin the analysis of population genetic structure of our Mexican collections, in conjunction with the global collection. We will submit our paper regarding the geographic and environmental distribution of chile in Mexico. For AIM II, we will begin to use the sequencing data generated in AIM I to create initial demographic models, which will allow us to begin assessing the chile pepper genome for regions that appear to have undergone selection. We will analyze the diversity in global landrace collection, exploring differences between and within species as predicted by structure outliers. We will also explore any potential associations with environmental variation. For AIM III, we will nearly complete the creation of F4:5 populations from our US x Mexico crosses and continue crossing and advancing the populations for the Within Mexico crosses, in part with seed newly imported from Mexico. We plan to genotype F4 individuals so that F5 families can be phenotyped.
Impacts
What was accomplished under these goals?
This past year (3/2020-2/2021) was dominated by the global COVID-19 pandemic. All three of our institutions were shut down for a period. While much of the on-site research in the US could restart in 2021, our Mexican colleagues remain (as of writing this report) with little lab access. Nevertheless, we were able to make progress on our research aims. AIM I: Determine the population genetic structure of chile pepper collections from the center of origin and diversity and its relationship with geographic and environmental factors We have advanced this first aim in three ways. First, in order to fine-tune the bioinformatics pipeline we will use once all of our chile pepper collections can be sequenced, we processed GBS data for 95 accessions that had already been genotyped. Based on a filtering process, we obtained an average of 4.5 million quality-filtered reads per sample (phred scale >30) that we additionally trimmed and filtered. We retrieved 160,252 high quality and informative SNPs. Second, we were able to use our time isolated from our labs to better understand the range of environments and geographic distribution of wild, semiwild, landrace, and commercial chiles from our Mexico collections. We had collected GPS coordinates which allowed us to utilize corresponding climatic data (e.g., bioclim variables) to track the environmental space from which we were sampling. We were able to create maps to visualize the geographic distribution of wild, semiwild, landrace and commercial chile pepper using MaxEnt modeling; then we extracted environmental parameters from those distributions to clarify the environmental space utilized by these different pepper types. We have now initiated a manuscript on this topic, which additionally explores the expected change in geographic distribution of each type with climate change. Third, we analyzed genotyping by sequencing (GBS) data acquired from one of our co-PIs from 467 landraces of chile pepper collected and sourced from seed sellers from across the globe. We plan to compare their genetic structure to that of our recent collections in Mexico. The GBS sequence of global collection will be made publically available. AIM II: Identify and characterize loci involved in environmental adaptation (especially to drought), ascertain their putative function, and discern the geographic distribution of their alleles Since we did not yet have DNA sequence data from Aim I to use for analyses of our overall collection, during this year we worked with data from a subset of our collection from the Mexican state of Oaxaca, which had already been sequenced (Taitano et al. 2019). Given its diversity, Oaxaca is a mesocosm of sorts for the work we plan to do with Mexico as a whole. We worked with this Oaxaca data to clarify loci involved in adaptation to abiotic stress in two ways: First, we worked on the manuscript detailing our previously performed environmental association analysis (EAA) to identify potentially adaptive loci for extreme environments. We had previously made associations between genetic variation and environmental variation discerned from the locations of origin of the lines. Multiple loci had been found to be associated with precipitation variables, which may mean that they may be relevant to drought tolerance. We identified five priority loci, three of which are found in the same region of the chromosome (or haplotype block)--an interesting convergence. Loci identified in this manuscript can be compared to loci we find through current analyses in Aims II and III. Second, since three priority loci from the EAA noted above were found in one haplotype block, we have worked to sequence portions of that haplotype block in various chile accessions, including the accessions from the US and Mexico that will be used as parents in Aim III. This work remains ongoing. AIM III: Locate quantitative trait loci (QTL) affecting phenology, physiology, and agronomic performance under drought in the greenhouse (GH) in Mexican and US materials We continue to be constrained in this aim due to both human and plant pandemics. Prior to COVID-19, our ability to import chile pepper seeds from Mexico to the US was hampered by new APHIS regulations https://www.aphis.usda.gov/import_export/plants/plant_imports/federal_order/downloads/2019/DA-2019-21.pdf. Due to viroids passed through pepper seeds, we need an official test in Mexico before exporting. The viroid testing is new for Mexican phytosanitary authorities, but we identified an official government lab to test seeds, worked with the lab on a protocol for testing our smaller seed batches, and determined that we can import the seeds to the US with the appropriate phytosanitary documentation of the testing. The testing is costly, but we are focusing our efforts on moving the most important accessions between Mexico and the US (those for Aim III). We are hopeful that we will have successfully tested, exported, and imported a new batch of seeds by August, 2021. First, we advanced the creation of Within Mexico populations for QTL analysis on two fronts. On the first front, we sourced seeds from our OSU accessions that represented the most divergent environments of origin (very dry vs very wet). Seven parental lines from dry and wet areas of Mexico were used to create F1 individuals, which led to one population being advanced to the F2; currently more F1 plants are being created and the number F2 seeds are being increased. On the second front, to increase the number of wet and dry parents that can be used for our Within Mexico crosses, we have prioritized importation from Mexico (with testing) of six accessions that would be preferrable partents. Once they are imported to Ohio, we will send them to Hawaii for crossing. Regarding the creation of RIL populations for the US x Mexico crosses for QTL analysis, we aim to produce segregating populations from parents that differ in drought tolerance to allow for QTL analysis of drought tolerance (AIM III). Having created 27 unique F1 individuals prior to the pandemic from US cultivars and Mexican accessions expected to have some drought tolerance, we have now developed a total of 37 F2 populations thus far and have advanced four populations to an F3. Some of the interesting crosses that are in these potential populations are crosses from parents that both have some degree of drought tolerance, but in different ways. We expect to have sufficient F4:5 seeds available to initiate the first QTL study in June 2022. We analyzed the experiment evaluating parents of the US x Mexico crosses under water deficit in the greenhouse. Although many phenotypic metrics were affected by water deficit, we found that accessions varied in how primary branch number and CO2 assimilation responded to drought. One US (Canoncito) and one Mexico accession (Ca0344) seem especially promising regarding their drought tolerance and we have prioritized the Canoncito x Ca0344 cross, among others, to advance to the F4:5 generation for the QTL study. We have been preparing this manuscript. The work we have done so far will enhance our understanding and conservation of chile pepper diversity. In particular, it provides a strong base from which to accomplish our current proposed research and also to launch future research projects on the domestication and evolution of chile pepper. The work here also demonstrates an opportunity to show how to respectfully conduct international research in the United States.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Bernau, V., L. Jard�n-Barbolla, L. McHale, and K.L. Mercer. 2020. Germination response of diverse wild and landrace chile peppers (Capsicum spp.) under drought stress under drought stress simulated with polyethylene glycol. PLOS ONE. doi.org/10.1371/journal.pone.0236001
|
Progress 03/01/19 to 02/29/20
Outputs
Target Audience:The work from all objectives serves the academic community interested agrobiodiversity generally, genetic diversity in crops, and the ways that past use and environment influence their diversity. Farmers utilizing landrace diversity in their cropping systems and those looking to increase diversity would also be interested. Additionally, our work is also of interest to the international NGO and research institute community around the globe working with landraces, as well as regulators and other interested parties. Finally, our work is of interest to those working in pre-breeding of crops with particular adaptations to abiotic stress and those looking to understand the evolution of local adaptation in plants. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?These activities provided training in field collection of crop genetic resources, including appropriate interactions with Mexican farmers and community members. Training was also received in molecular genetic techniques, greenhouse propagation, crossing, experimental design, and pepper breeding. It provided an opportunity to explore plant genetic resources and the implications of the international treaty on plant genetic resource on plant breeding and conservation. A graduate student was able to attend an academic meeting and made presentations within the university. How have the results been disseminated to communities of interest?We primarily disseminate our work through publication of our research results in peer reviewed journals, as well as through professional conferences. What do you plan to do during the next reporting period to accomplish the goals?Regarding AIM I, we will extract data from and genotype wild and landrace collections from throughout Mexico. We will analyze the population genetic structure of our Mexico collections, as well as the global collection. We will continue to work on our paper regarding the geographic and environmental distribution of chile in Mexico and how our collection compares. For AIM II, using the DNA generated in AIM I from the Mexican chile pepper collections, we will create our initial demographic models to enable our analyses and begin assessing the chile pepper genome for portions that appear to have undergone selection. For AIM III, we will complete the creation of F4:5 populations from our US x Mexico crosses and initiate the crosses for the Within Mexico crosses.
Impacts
What was accomplished under these goals?
AIM I: Determine the population genetic structure of chile pepper collections from the center of origin and diversity and its relationship with geographic and environmental factors During this past year (3/2019 - 2/2020), we focused our collections in Mexico in El Bajío Region, Veracruz, Northwestern Mexico (including Baja California and the Sonora-Sinaloa Coast), Sierra Gorda de Querétaro, a Tabasco-Chiapas transect, and the Yucatan peninsula. As a result, we now have a total of 1156 accessions that were sampled from nearly all Mexican chile growing regions. This range encompasses the semi dry and commercial plantations from Northwestern Mexico, to seasonal wild populations both in northwestern and central Mexico, as well as the tropical-humid zones of southern and eastern Mexico. In total, we made seven field collection trips during this last year. To enhance our collection, we got previously collected accessions from researchers in Mexico to avoid duplicating their work and to avoid traveling to dangerous zones in Mexico (e.g., much of northern Mexico). We received about 100 accessions to supplement our collection efforts. Our collections cover the range of environmental conditions where chile pepper can be found growing in Mexico. In order to capture this, for all accessions, we collected data on the state, region, community, and farmer from which we had collected. We also noted the GPS coordinates, elevation, species, type (wild/cultivated, landrace name), and the type of cultivation system from which it was collected (backyard, milpa, plantation, forest). Importantly, the GPS coordinates also allowed us to map our collection locations to produce visuals of climatic data from collection points (e.g., bioclim variables) to track the environmental space from which we were sampling. Thus, we visualized the environmental breadth and representativeness of our collection. We have initiated a manuscript aiming to evaluate the geographic and environmental distribution of wild and cultivated chile pepper in Mexico, the expected change in geographic distribution with climate change, and how well our collections represent current and future distributions. In total, we have collected different 85 locally named chile landraces; many of these names are actually local variants on the same basic type. Taking that into account, our collections cover all but five of the 68-70 major agronomic landraces reported in the agronomic literature for Mexico. A reason for our abundance of locally named types arises from our exhaustive sampling of backyard and small plot populations where local names abound. Some of these landraces are now quite rare (e.g., Yaax'ik and Chawa ik Pais in the Yucatan). We also have collected 60 wild populations, totaling 307 accessions. As a group, we have been discussing these collections extensively to ensure that we are sampling across the greatest range of environments possible in Mexico. Our sampling now covers 23 out of 32 Mexican states, with heaviest coverage in Oaxaca and Yucatán--two hotspots of chile pepper diversity. Regarding DNA extraction, we have been germinating seeds from our collections in order to then extract their DNA. The emphasis has thus far been on sequencing the wild chile collection--probably the most unique aspect of our overall collection. So far, we have genotyped 94 accessions, corresponding 26 accessions of 22 landraces and 68 accessions belonging to C. annuum var. glabrisculum, either semi-wild (21) or wild (47). We are developing a plan to prioritize particular collections for further sequencing. Thus, our key outcomes are that we made extensive collections of chile pepper from throughout Mexico and have begun extracting DNA and sequencing accessions. The sequenced DNA from these diverse collections will help us analyze the overall genetic structure of chile pepper populations in Mexico and the degree to which environmental conditions play a role in organizing that variation. AIM II: Identify and characterize loci involved in environmental adaptation (especially to drought), ascertain their putative function, and discern the geographic distribution of their alleles We did not advance in this aim during this time period. All the work of AIM II relies on the DNA extracted and sequenced from our collections made in AIM I. AIM III: Locate quantitative trait loci (QTL) affecting phenology, physiology, and agronomic performance under drought in the greenhouse (GH) in Mexican and US materials The major activities we completed towards this goal center around (1) initiating the Within Mexico crosses with identified parents, (2) advancing the RILs (recombinant inbred lines) from our US x Mexico crosses, and (3) evaluating the initial parents from the cross in #2 for drought tolerance traits in the GH. To identify parents for our Within Mexico crosses, we used environmental data from our Mexico-wide collections to seek out collections from similar temperature zones, but which experienced the extremes of precipitation--very dry or very wet. We used a Shiney app coded in R by our team to facilitate this process. Unfortunately, our ability to import chile pepper seeds from Mexico to the US has been hampered by regulations from APHIS imposed August 9, 2019 due to problematic viroids that can be passed by pepper seeds. Since that time, we have not been able to import seeds due to the need for an official viroid test in Mexico before exporting. We continue to work on this; for now, we are using only seeds that were already in the US when this order was imposed. See the order here: https://www.aphis.usda.gov/import_export/plants/plant_imports/federal_order/downloads/2019/DA-2019-21.pdf Regarding the creation of RIL populations for the US x Mexico crosses, we aim to produce segregating populations from parents that differ in drought tolerance to allow for QTL analysis of drought tolerance (AIM III) and affirmation of genetic variants that we identify through population genetic and genome wide association analyses (in AIMS I & II). To this end, we grew 39 different US cultivars along with 15 lines sourced from Mexican collections that showed drought tolerance and sequenced their DNA. We completed the F1 crosses between US and Mexican parents and selfed the parents, as well. We created 27 unique F1 individuals, reflecting differential success of crosses between parental combinations. We have set up a speed breeding approach in growth chambers to rapidly cycle through generations to get to F4:5. We have developed a total of 37 F2 populations thus far. We have advanced five populations to an F3 and are currently creating one F4 population. To advance our Within Mexico crosses, seven parental lines from dry and wet areas of Mexico are currently being grown with plans to create F1 crosses soon. Regarding phenotypic and genetic evaluation of the parents of the US x Oaxaca crosses, we grew out the parents in a drought experiment, either watering plants daily or weekly. We found variation among Mexican and US accessions for their ability to withstand water deficit. Using DNA extracted from the parents, we also began the process of genotyping the parents at putative drought tolerance loci identified in our preliminary research. Knowing about the drought tolerance phenotypes of parents, as well as their genotypes at drought tolerance loci will allow us to best choose the crosses to advance to the F4:5 generation for the QTL study. Additionally, we have sequenced DNA from 500 landraces from across the globe sourced from seed sellers to be able to compare their genetic structure to that of our recent collections in Mexico. We hope to genotype them at the genetic variants we find to be associated with drought tolerance to explore how widespread drought tolerance is in cultivated peppers.
Publications
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2019
Citation:
J, McCoy, K. Mercer, and L. McHale. Evaluating Drought Tolerance in Pepper (Capsicum sp.) from the U.S. and Mexico Poster American Society of Horticultural Science Annual Conference, July 2019
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2019
Citation:
Genomics and Geography: Leveraging Big Data to Improve Agricultural Sustainability, MIGAL Galilee Research Institute, Kiryat Shmona, Israel
|
Progress 03/01/18 to 02/28/19
Outputs
Target Audience:The work from all objectives serves the academic community interested agrobiodiversity generally, genetic diversity in crops, and the ways that past use and environment influence their diversity. Farmers utilizing landrace diversity in their cropping systems and those looking to increase diversity would also be interested. Additionally, our work is also of interest to the international NGO and research institute community around the globe working with landraces, as well as regulators and other interested parties. Finally, our work is of interest to those working in pre-breeding of crops with particular adaptations to abiotic stress and those looking to understand the evolution of local adaptation in plants. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?These activities provided training in field collection of crop genetic resources, including appropriate interactions with Mexican farmers and community members. Training was also received in molecular genetic techniques, greenhouse propagation, experimental design, and pepper breeding. It provided an opportunity to explore plant genetic resources and the implications of the international treaty on plant genetic resource on plant breeding and conservation. A graduate student was able to attend a training on the use of new equipment for measuring physiological status of plants. How have the results been disseminated to communities of interest?We primarily disseminate our work through publication of our research results in peer reviewed journals, as well as through professional conferences. What do you plan to do during the next reporting period to accomplish the goals?Regarding AIM I, we will finish the sampling trips within Mexico, as well as get seed and/or DNA from collaborators at the University of Aguascalientes and the Autonomous University of Baja California who have collected wild and cultivated chile from northeast and northwest Mexico. In particular, we plan to perform: one collecting trip to the Sierra Gorda de Querétaro and the Bajío region, in Central México (late July, 2019); one sampling trip to Chiapas and Tabasco in southern Mexico (early-mid September, 2019); and one sampling trip to Yucatán Peninsula (mid-november, 2019). We will also genotype the wild and landrace collections and someone from Dr. Jardon's team will get trained on molecular analyses. For AIM II, using the DNA generated in AIM I from the Mexican chile pepper collections, we will create our initial demographic models to enable our analyses. For AIM III, we will complete the creation of F4:5 populations from our US x Oaxaca crosses and initiate the crosses for the Within Mexico crosses. To hasten the choice of parents for the latter, we will track the environments from which we have collected to find accessions that come from the wettest and driest areas to possibly use as parents.
Impacts
What was accomplished under these goals?
AIM I: Determine the population genetic structure of chile pepper collections from the center of origin and diversity and its relationship with geographic and environmental factors The major activities we completed towards this aim included the collection of accessions of chile pepper from across Mexico and the initiation of DNA extraction. Regarding collections, Lev Jardon-Barbolla at UNAM and his team have spearheaded the expansion of the collection of Capsicum annuum landraces and wild plants into areas of Mexico that we had not yet collected (e.g., the state of Chiapas, the Bajío region, and the Yucatan peninsula). Doing so has meant that we now have more collections, but also that those collections sampled a wider range of environmental conditions, as well as agroecosystem management practices, than did previous collections. Our collections included ones from the cold, dry area of Bajío, as well as from the hot Yucatan peninsula, which encompasses a rainfall gradient. For all collections, we collected data on the state, region, community, and farmer from which we had collected. We also noted the GPS coordinates, elevation, species, type (wild/cultivated, landrace name), and the type of cultivation system from which it was collected (backyard, milpa, plantation, forest). The GPS coordinates also allow us to map our collection locations and produce graphs using the climatic data (bioclim variables) known about collection points, to track the environmental space from which we are sampling. To enhance our collections, Drs. Jardon-Barbolla and Mercer also communicated with researchers in the US and Mexico about acquiring collections they have previously made in other regions to avoid duplicating their work and to avoid traveling to dangerous zones in Mexico (e.g., much of northern Mexico). We have not completed all planned collections and will continue to collect this year, especially in the states of Chiapas and Tabasco, as well as back in the Yucatan, an especially interesting area for collecting wild chile peppers in the forest. However, we have collected 40 different chile landraces (out of 68-70 landraces reported in the agronomic literature for Mexico), as well as a number of wild populations, totaling 187 accessions. Some of these landraces are now quite rare (e.g., Yaax'ik in the Yucatan). As a group, we have been discussing these collections a lot to ensure that we are sampling across the greatest range of environments possible in Mexico. Regarding DNA extraction, Dr. Jardón-Barbolla and his technician have begun to germinate seeds corresponding to 64 of the sampled accessions in order to then extract their DNA. We will collect fresh tissue from these plants and start DNA extraction soon. For now, we are optimizing our DNA extraction techniques and working on our plants for DNA sequencing. Thus, our key outcomes are that we have made extensive collections of chile pepper from throughout Mexico and that the process of DNA extraction is under way. The sequenced DNA from these diverse collections will help us analyze the overall genetic structure of chile pepper populations in Mexico and the degree to which environmental conditions play a role in organizing that variation. AIM II: Identify and characterize loci involved in environmental adaptation (especially to drought), ascertain their putative function, and discern the geographic distribution of their alleles We did not advance in this aim during this time period. All the work of AIM II relies on the DNA extracted and sequenced from our collections made in AIM I. Thus, the work mentioned above in AIM I will help us identify and characterize loci involved in environmental adaptation in this system. AIM III: Locate quantitative trait loci (QTL) affecting phenology, physiology, and agronomic performance under drought in the greenhouse (GH) in Mexican and US materials The major activities we completed towards this goal center around identifying appropriate parents for our US x Oaxaca crosses, initiating the creation of RILs (recombinant inbred lines) from these crosses, and evaluating the initial parents genetically and for drought tolerance. To identify parents for our crosses, a graduate student in the labs of Drs. Mercer and McHale identified previously collected accessions from Oaxaca, Mexico that came from dry areas and also showed some drought tolerance in prior greenhouse studies. Dr. Mercer's undergraduate and Dr. Kantar identified US varieties that were off PVP (from seed companies and the USDA GRIN system) and suspected to possess little drought tolerance to use for our US x Oaxaca crosses. Regarding working towards the creation of RIL populations, Dr. Kantar and his team (including two graduate students) have now spearheaded F1 crosses between types, as well as selfing of the parents. The F1 crosses will ultimately lead to production of segregating populations from parents that differ in drought tolerance to allow for QTL analysis of the drought tolerance and affirmation of genetic variants that we identify through population genetic and genome wide association analyses (in AIMS I & II). To this end, Dr. Kantar grew 39 different US cultivars sources. We grew these lines with 15 lines sourced from Mexican Collections that showed drought tolerance and some insect resistance and sequenced their DNA. From the potential crosses we created 27 unique F1 individuals, reflecting differential success of crosses between parental combinations. We also self-pollinated each plant to maintain their line. F1 plants are currently flowering in the greenhouse at University of Hawaii. When fruit from F1 plants is harvested we have set up a speed breeding approach in growth chambers to rapidly cycle through generations to get to F4:5. Additionally, we have extracted DNA from 500 landraces from across the globe and plan to genotype them at the genetic variants associated with drought tolerance, to explore how widespread drought tolerance is in cultivated peppers. Regarding phenotypic and genetic evaluation of the parents of the US x Oaxaca crosses, a graduate student from the labs of Drs. Mercer and McHale at the Ohio State University has begun to grow out the parents in a drought experiment. Using DNA extracted from the parents by Dr. Kantar, the graduate student will also genotype the parents at putative drought tolerance loci identified in our preliminary research. Knowing about the drought tolerance phenotypes of parents, as well as their genotypes at drought tolerance loci will allow us to best choose the crosses to advance to the F4:5 generation for the QTL study. Two undergraduates are slated to perform independent research on spin-offs of this work especially dealing with root morphology.
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