Data from: The genetic architecture of quantitative variation in the self-incompatibility response within Phlox drummondii (Polemoniaceae)
Data files
Jun 19, 2025 version files 2.08 GB
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GenoPheno.csv
2.64 MB
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linkage_map.csv
393.34 KB
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README.md
3.96 KB
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S1.bam
312.38 MB
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S2.bam
627.74 MB
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S3.bam
247.72 MB
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S4.bam
384.09 MB
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S7.bam
210.71 MB
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S9.bam
292.89 MB
Abstract
Flowering plants display extensive variation in selfing rate, a trait with significant ecological and evolutionary consequences. Many species use genetic mechanisms to recognize and reject self-pollen (termed self-incompatibility or SI), and the loss of SI is one of the most common evolutionary transitions among flowering plants. Despite the ubiquity of transitions to self-compatibility (SC), little is known about the genetic architecture through which SC evolves. Specifically, it is important to determine if SC has a polygenic or simple genetic basis and if variation in compatibility localizes to the genomic locus causing self-pollen recognition (the “S-locus”). Phlox drummondii (Polemoniaceae) has been a model system for exploring mating system evolution and expresses extensive range-wide variation in the SI response. Here we investigate the genetic architecture of SC variants segregating within this otherwise SI species. Using multiple independent crosses, we uncover numerous QTLs associated with intraspecific variation in SI, consistent with a polygenic genetic architecture. While some QTLs overlap across mapping experiments, other QTLs are unique, suggesting that multiple genetic routes to SC exist. Through these crossing experiments, we demonstrate that P. drummondii has a sporophytic SI system, suggesting that an independent evolution of SI occurred in the lineage containing Phlox. We map this novel S-locus and find that the genomic region containing the S-locus is associated with intraspecific variation in SI in one of the three mapping populations. Although further work is necessary to clarify the conditions under which quantitative variation in SI represents a transitional pathway to complete SC, our study reveals the underlying genetic architecture upon which selection could act to drive this frequent and evolutionarily significant transition.
Dataset DOI: 10.5061/dryad.7m0cfxq73
Description of the data and file structure
Title: "The genetic architecture of quantitative variation in the self-incompatibility response within Phlox drummondii (Polemoniaceae)"
Authors: Grace A. Burgin1,, Federico Roda1,2, Matthew Farnitano1,3, Charles Hale1,4, Antonio Serrato-Capuchina1,5, Robin Hopkins1,
1. Department of Organismic and Evolutionary Biology, The Arnold Arboretum, Harvard University, Cambridge MA, USA
2. Current affiliation, Max Planck Tandem Group in Evolutionary Genomics of Specialized Metabolism, Universidad Nacional de Colombia, Bogotá, Colombia
3. Current affiliation, Department of Genetics, University of Georgia, Athens GA, USA
4. Current affiliation, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY USA 14853
5. Current affiliation, Department of Biology, Boston College, Boston MA, USA
*correspondence to: grace_burgin@fas.harvard.edu, rhopkins@fas.harvard.edu
This dataset contains linkage map, phenotype-genotype tables, and .bam files used to investigate the genetic basis of infraspecific variation in self-incompatibility within Phlox drummondii flowers.
Files and variables
File: linkage_map.csv
Description: linkage map used for QTL mapping of Family A
Variables
- V1: linkage group name (1-7 in the Phlox genome)
- V2: genomic position in Mb (indexing beginning with 0)
- V3: genomic position in Mb (indexing beginning with 1)
- V4: genomic position in cM
- positions_linkage: unique ID for each marker used in QTL
File: GenoPheno.csv
Description: genotypes and phenotypes used for QTL mapping of Family A
Variables
- ID: unique ID given to each F2 in the Family A mapping population
- Self_crosses: Number of flowers crossed with self-pollen
- Self_seedset: Number of self-seeds set
- Outcrosses: Number of flowers crossed with outcross pollen
- Outcross_seedset: Number of outcross seeds set
- Columns F through JRR: Gives the genotype for each individual at each marker from the linkage map (see "positions_linkage in linkage_map.csv)
- Row 2: linkage group
- Row 3: genomic position in cM
- Row 4 through 172: each individual's genotype at each marker (H=heterozygous, A=homozygous for parent A genotype, B=homozygous for parent B genotype, -=no data)
File: S4.bam
Description: Family B, genotype S2S2. BAM files of bulk segregant (BSA) mapping. Reads were aligned to the Phlox drummondii assembly available at doi.org/10.5281/zenodo.15498773
File: S1.bam
Description: Family C, genotype S3S3. BAM files of bulk segregant (BSA) mapping. Reads were aligned to the Phlox drummondii assembly available at doi.org/10.5281/zenodo.15498773
File: S9.bam
Description: Family B, self-compatible. BAM files of bulk segregant (BSA) mapping. Reads were aligned to the Phlox drummondii assembly available at doi.org/10.5281/zenodo.15498773
File: S3.bam
Description: Family B, genotype S1S1. BAM files of bulk segregant (BSA) mapping. Reads were aligned to the Phlox drummondii assembly available at doi.org/10.5281/zenodo.15498773
File: S7.bam
Description: Family C, self-compatible. BAM files of bulk segregant (BSA) mapping. Reads were aligned to the Phlox drummondii assembly available at doi.org/10.5281/zenodo.15498773
File: S2.bam
Description: Family C, genotype S4S4. BAM files of bulk segregant (BSA) mapping. Reads were aligned to the Phlox drummondii assembly available at doi.org/10.5281/zenodo.15498773
Access information
Other publicly accessible locations of the data:
- Reference genome and genome annotation files available at doi.org/10.5281/zenodo.15498773