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Development of first linkage map for Silphium integrifolium (Asteraceae) enables identification of sporophytic self-incompatibility locus

Abstract

Silphium integrifolium (Asteraceae) has been identified as a candidate for domestication as a perennial oilseed crop and is assumed to have sporophytic self-incompatibility system—the genetic basis of which is not well understood in the Asteraceae. To address this gap, we sought to map the genomic location of the self-recognition locus (S-locus) in this species. We used a biparental population and genotyping-by-sequencing to create the first genetic linkage map for this species, which contained 198 SNP markers and resolved into the correct number of linkage groups. Then we developed a novel crossing scheme and set of analysis methods in order to infer S-locus genotypes for a subset of these individuals, allowing us to map the trait. Finally, we evaluated potential genes of interest using synteny analysis with the annual sunflower (Helianthus annuus) and lettuce (Lactuca sativa) genomes. Our results confirm that S. integrifolium does indeed have a sporophytic self-incompatibility system. Our method is effective and efficient, allowed us to map the S. integrifolium S-locus using fewer resources than existing methods, and could be readily applied to other species.

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Fig. 1: Visualization of the crossing design used in this experiment.
Fig. 2: Linkage map for Silphium integrifolium.
Fig. 3: Distribution of seed set values for reciprocal matings (pairs of individuals mated, with each individual used as both a male and female).
Fig. 4: Representation of all possible matings that could have been completed for this study, with each square representing one pairing.

Data availability

All code and data to replicate analyses may be found on GitHub, at https://github.com/UMN-BarleyOatSilphium/SilphiumSLocus. All sequence data may be accessed under BioProject PRJNA695552.

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Acknowledgements

Funding for this work was provided by The Perennial Agriculture project in conjunction with The Land Institute and the Malone Family Land Preservation Fund, the United States Department of Agriculture’s National Institute of Food and Agriculture Grant no. 2019-67011-29607 to JHP, the Minnesota Department of Agriculture - Forever Green Agricultural Initiative, and NSF grant #1737827 Dimensions US-China to YB. The authors thank Shannon Lee Anderson, Karen Beaubein, and Jill Ekar for their help in completing the controlled crosses for this experiment. In addition, the authors thank Dr. Kevin Dorn for assistance in developing a GBS protocol, Dr. Adam Herman for bioinformatics advice, and Dr. Owen Beisel for inspiring the hill-climbing algorithm method. Finally, the authors acknowledge the Minnesota Supercomputing Institute (MSI) at the University of Minnesota for providing computing resources that contributed to the analysis of this study.

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Contributions

The effort to develop a linkage map was initiated by KPS, DLVT, and YB, who also secured initial funding. DLVT created the mapping population, contributed text, and visualization, and provided feedback in writing. JHP constructed the linkage map, initiated and designed the S-locus mapping work, and developed the HC method. ARR developed the MCMC method. JHP and ARR conducted data analysis and wrote the manuscript. KPS and YB provided supervision, and feedback on analysis, writing, and visualization.

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Correspondence to Kevin P. Smith.

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Price, J.H., Raduski, A.R., Brandvain, Y. et al. Development of first linkage map for Silphium integrifolium (Asteraceae) enables identification of sporophytic self-incompatibility locus. Heredity 128, 304–312 (2022). https://doi.org/10.1038/s41437-022-00530-4

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