Patterns of genetic variation in a prairie wildflower,Silphium integrifolium, suggest a non-prairie origin and locally adaptive variation

Abstract

Patterns of genetic variation in a prairie wildflower, Silphium 1 integrifolium, suggest a non-prairie origin and untapped variation 2 available for improved breeding.Abstract 9 Premise 10 Understanding the relationship between genetic structure and geography provides 11 information about a species' evolutionary history and can be useful to breeders interested 12 in de novo domestication. Silphium integrifolium is an iconic perennial American prairie 13 wildflower that is targeted for domestication as an oilseed crop. Germplasm in the existing 14 breeding program is derived from accessions collected in restricted geographic regions. We 15 present the first application of population genetic data in this species to address the 16 following goals (1) improve existing breeding programs by characterizing genetic structure 17 and (2) identify the species geographic origin and potential targets and drivers of natural 18 selection as the range has expanded. 19 Methods 20We developed a reference transcriptome to use as a genotyping reference for dozens of 21 samples from throughout the species range. Population genetic analyses were used to 22 describe the distribution of genetic variation and demographic inference modeling was used 23 to characterize potential processes that have shaped variation. Divergence outlier scans for 24 selection and associations with environmental variables were used to identify loci linked to 25 putative targets and drivers of natural selection. 26 Key results 27 Genetic variation partitions samples into three geographic clusters. Patterns of variation 28 and demographic modeling suggests that the geographic origin of the species is in the 29 American southeast. Breeding program accessions are from the region with lowest observed 30 genetic variation. 31 Conclusions 32 This iconic prairie species did not originate within the modern prairie. Breeding programs 33 can be improved by including accessions from outside of the germplasm founding region, 34 which has relatively little genetic variation compared to the south and east. The observed 35 geographic structuring of variation coupled with the identified targets and environmental 36 drivers of adaptation during range expansion can guide future collecting efforts towards 37 wild populations with beneficial agronomic traits.38

Assessing phenotypic diversity in silflower (Silphium integrifolium Michx.) to identify traits of interest for domestication selection

“…The Land Institute breeding program was founded primarily using germplasm collected from the Kansas area, which represents only a fraction of the native distribution of S. integrifolium (Vilela et al., 2018). Additionally, the Kansas subpopulation may show decreased diversity relative to other wild populations, particularly those in the southern United States (Raduski et al., 2021). The SDP may be thought of as a valuable resource to begin refining breeding populations that conform to possible ideotypes, but introgressing variation from wild populations into this base will be crucial.…”

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

“…Any genes homologous to known CRPs were also considered potential candidates (Marshall et al, 2011). The best homologs for a subset of these candidates were then identified in the S. integrifolium reference transcriptome (Raduski et al, 2021), and their expression was measured in a previously-published set of whole-plant seedling transcriptomes from a diversity panel of 73 wild collected S. integrifolium accessions (Raduski et al, 2021). Expression was quantified in total transcripts per million (TPM), TPM as a percentile of total expressed genes, and TPM as a percentile of a reference set of conserved single copy genes, known as BUSCO (which was not certified by peer review) is the author/funder.…”

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

“…Any genes homologous to known CRPs were also considered potential candidates (Marshall et al, 2011). The best homologs for a subset of these candidates were then identified in the S. integrifolium reference transcriptome (Raduski et al, 2021), and their expression was measured in a previously-published set of whole-plant seedling transcriptomes from a diversity panel of 73 wild collected S. integrifolium accessions (Raduski et al, 2021). Expression was quantified in total transcripts per million (TPM), TPM as a percentile of total expressed genes, and TPM as a percentile of a reference set of conserved single copy genes, known as BUSCO (Simão et al, 2015).…”