Source: THE MISSOURI BOTANICAL GARDEN submitted to
GENOMIC STRUCTURAL VARIATION IN SUNFLOWER: DIVERSITY UNDER DOMESTICATION AND IMPORTANCE FOR STRESS TOLERANCE
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1028346
Grant No.
2020-67034-36879
Cumulative Award Amt.
$93,185.63
Proposal No.
2021-12748
Multistate No.
(N/A)
Project Start Date
Sep 1, 2021
Project End Date
Jun 30, 2023
Grant Year
2022
Program Code
[A7201]- AFRI Post Doctoral Fellowships
Project Director
Warschefsky, E.
Recipient Organization
THE MISSOURI BOTANICAL GARDEN
2345 TOWER GROVE AVE
SAINT LOUIS,MO 631103420
Performing Department
William L. Brown Center
Non Technical Summary
This project (Project Director: Emily Warschefsky) will identify SV in the cultivated and wild H. annuus genome that have been the target of selection, introduced via introgression, or are associated with adaptation to particular environmental conditions. Additionally, SV that contribute to genetic load in sunflower will be identified. Furthermore, this project will test whether SV has changed the correlations between agriculturally important traits, such as seed dimensions. As such, in line with the AFRI priority area: Plant health and production and plant products, the results of this project will provide foundational knowledge to all crop breeding programs and will directly benefit sunflower breeding practices.
Animal Health Component
15%
Research Effort Categories
Basic
85%
Applied
15%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
20118441080100%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1844 - Sunflower;

Field Of Science
1080 - Genetics;
Goals / Objectives
This project will identify SV in the cultivated and wild H. annuus genome that have been the target of selection, introduced via introgression, or are associated with adaptation to particular environmental conditions. Additionally, SV that contribute to genetic load in sunflower will be identified. Furthermore, this project will test whether SV has changed the correlations between agriculturally important traits, such as seed dimensions. As such, in line with the AFRI priority area: Plant health and production and plant products, the results of this project will provide foundational knowledge to all crop breeding programs and will directly benefit sunflower breeding practices.Scientific Aims1. Identify and characterize SV in domesticated and wild H. annuus.Both the Kane (Primary mentor) and Rieseberg (Collaborating mentor) labs were recently involved in publishing the first pan- genome for sunflower (Hu?bner et al., 2019), which focused on the gene space only. In this aim, I will identify and characterize inversions, CNV, and PAV in wild, landrace, and modern lines of H. annuus.2. Identify SV associated with selection, introgression, and the cost of domestication.Domestication involves multiple evolutionary processes that impact the genomic diversity of crop species. Traditionally, domestication genomics examines a few main phenomena: the loss of genetic diversity associated with population bottlenecks during domestication and improvement selective sweeps for traits associated with the domestication syndrome, and historical and modern introgression between crops and their wild relatives, all of which impact the genetic diversity of modern crops. More recently, domestication research has also begun to explore the accumulation of deleterious mutations in domesticated lineages that result from selection and demographic processes; a phenomenon termed the cost of domestication. In this aim, I will identify SV in cultivated H. annuus that have been the targets of selection and/or have been introduced by introgression during the domestication process and estimate the cost of domestication associated with these SV.3. Connecting SV to agriculturally relevant phenotypes in sunflowerRelatively few studies have directly associated SVs with particular phenotypes using genome wide association (GWA) studies, but those that have demonstrate that SV may have a disproportionately large effect on phenotype compared to SNPs, and can impact agriculturally relevant phenotypes from reproductive morphology to seed color, plant height, and nematode resistance. In this aim, I will identify SV that are linked to important agricultural phenotypes and environmental tolerance in cultivated H. annuus. Data from wild and cultivated (combined landrace and modern) H. annuus is available for a number of agricultural traits, including seed traits, plant architecture, flowering time, vegetative traits, developmental traits, and abiotic and biotic stress tolerance. Additionally, geographic locations and environmental data are available for the collections of wild H. annuus.?
Project Methods
MethodsThe project will be conducted as a collaboration between the PD, Primary, and Collaborating Mentors.Aim 1.a) The published pan-genome for sunflower will be improved by adding non-coding sequences using information from updated reference genomes for wild and cultivated lines. Using this augmented pan-genome, structural variants will be inferred across 1,298 samples of domesticated and wild H. annuus. Based on preliminary analysis, we expect there to be high levels of diversity in SV, even within cultivated lines.b) Genome-wide patterns and functional impacts of CNV, PAV, and inversions will be characterized and compared across wild, landrace, and modern H. annuus. Annotations from the HA412 and Han-B-XRQ genomes and the GOA database will be used to characterize the functional impacts of SV in the H. annuus genome, and a comparative gene ontology (GO) enrichment analysis of wild, landrace, and cultivated H. annuus will be performed.Aim 2.a) CNV, PAV, and inversions (Aim 1) will be associated with previously identified selective sweeps and introgressed regions in landrace and modern H. annuus. To explore the potential functional impacts of selective sweeps and introgression, I will also characterize and compare the GO of SVs that map to these regions.b) The mutational load of SV in H. annuus will be inferred to test the general hypothesis that SV contributes to the cost of domestication in crops and to identify particular SV within the sunflower genome that are putatively deleterious.Aim 3.a) SV associated with traits of agricultural importance will be identified by performing GWA analysis for the wild and cultivated populations using CNV, PAV, and inversions.b) Using a combination of genome-environment association (GEA), and GWA, particular phenotypes in the cultivated population of H. annuus will be linked to adaptation to particular environmental variables.c) Trait correlations and variance/covariance matrices (G-matrices) will be compared for all samples combined as well as within cultivated and wild populations separately. The genetic correlation between traits for each inversion haplotype will be calculated.Efforts: Results of this work will be disseminated to the scientific and sunflower breeding communities at scientific conferences, the PD meeting, and in peer-reviewed publicationsEvaluations: The project will be evaluated based on satisfactory completion of the goals according to the outline provided in the proposal.

Progress 09/01/21 to 06/30/23

Outputs
Target Audience:The target audiences of this work include the sunflower breeding community and researchers with an interest in the evolutionary dynamics and genomic impacts of domestication. To engage the scientific community, the PD co-organizedthe annual workshop on Domestication Genomics for the International Plant and Animal Genome Workshop, bringingtogether researchers who study the evolutionary dynamics of domestication across crops and livestock and facilitates the exchange of innovative ideas and methodologies. Furthermore, this work was presented to academic audiences at multiple University seminars. These target audiences will continue to be reached through scientific publications and presentations at targeted conferences, such as the Plant and Animal Genome Conference and the International Sunflower Symposium. Changes/Problems:The onset of this project during the early phase of COVID-19 proved to be a significant challenge that ultimately impacted the research schedule and goals of this project. Multiple factors, including the pandemic, the severe illness of a key team member, and delays in transferring funds during conversion from a postdoctoral award to a standard grant, interfered with the PD's ability to build and maintain the collaborative relationships required of this project. What opportunities for training and professional development has the project provided?This project provided a great deal of training and professional development for the PD. In terms of formal skills, the PD gained experience with bioinformatics, data management, and knowledge around methodologies for genomic analysis. Furthermore, the PD gained experience in critical skillsets of project management, mentorship, leadership, and working on collaborative research across multiple institutions. The PD was also able to participate in multiple workshops, including a DEI workshop through the University of Colorado Boulder.? How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? This project sought to identify and characterize structural variants (SV) within the genome of wild sunflower,Helianthus annuusin an effort to understand how this form of genomic variation responds to selection and domestication, and how SV impacts correlations between important agricultural traits such as seed dimension. Specifically, this project aimed to (1) identify and characterize SV in domesticated and wildH. annuus.Progress toward this aim was made in collaboration with CU Boulder and the USDA in Ames, IA. This involved work done by a MSc student and the PD to aggregate genomic datasets and generate a new pan-genome for sunflower to identify SV from the domesticated lines. Unfortunately, multiple unanticipated technical and logistic hurdles were experienced during this phase of the project and results are not yet complete. The project also aimed to (2) identify SV associated with selection, introgression, and the cost of domestication. While progress in the conceptualization of methods to be used for this portion of the project was made, they have not yet been implemented because of the delays in the accomplishment of the first aim. The final aim of the project was to (3) connect SV to agriculturally relevant phenotypes in sunflower. Because of the delays in accomplishing the previous aims, the planned activities and experiments around this aim were not completed.

Publications

  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Krug AS, B M Drummond E, Van Tassel DL, Warschefsky EJ. The next era of crop domestication starts now. Proc Natl Acad Sci U S A. 2023 Apr 4;120(14):e2205769120. doi: 10.1073/pnas.2205769120. Epub 2023 Mar 27. PMID: 36972445; PMCID: PMC10083606.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: The next era of crop domestication starts now. Presented at the Society for Economic Botany annual Conference, Atlanta, GA, USA. June 4-9, 2023.


Progress 09/01/21 to 08/31/22

Outputs
Target Audience:The target audiences of this work include the sunflower breeding community and researchers with an interest in the evolutionary dynamics and genomic impacts of domestication. The academic audiences have been engaged through seminars at Universities and the organization of the Domestication Genomics Workshop for the International Plant and Animal Genome Conference. Changes/Problems:This project has been more difficult to accomplish than anticipated, in part due to unanticipated technical challenges, but especially because of the pandemic. While it is based in bioinformatics and data analysis, it requires the collaboration of multiple individuals across different institutions. To facilitate these essential collaborations, the PD had intended to visit these collaborators in person to help move this project forward, but this was not possible, and has hindered progress. What opportunities for training and professional development has the project provided?The PD has gained experience with managing large-scale genomic datasets, bioinformatics pipelines, and analytic tools, in addition to building skillsets in project and time management, mentorship, and collaborative research projects. Additionally, in her new role, the PD has recruited two PhD students and begun to set up a molecular lab. How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals?Unfortunately, this project is behind schedule. As such, the PD hopes to reach out to strengthen the collaborations between involved institutions and personnel, as well as recruit additional personnel to help ensure the aims are accomplished.

Impacts
What was accomplished under these goals? Aim 1: Identify and characterize SV in domesticated and wild H. annuus. During this reporting period, progress was made toward this aim, including aggregation of genomic datasets and preliminary bioinformatics work to improve the existing pan-genome and identify structural variants. Further work is required to refine these results to enable them to be used for subsequent aims. Aim 2: Identify SV associated with selection, introgression, and the cost of domestication. During this reporting period, progress toward the accomplishment of these aims included identification of specific methodologies that may be used for these analyses. Aim 3: Connecting SV to agriculturally relevant phenotypes in sunflower. Because of the delays in accomplishing the earlier aims, progress toward this aim has not yet been made.

Publications