DOI: 10.5061/dryad.7m0cfxq73
title: Data from: The genetic architecture of quantitative variation in the self-incompatibility response within Phlox drummondii (Polemoniaceae)

description: 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.
description: # The genetic architecture of quantitative variation in the
 self-incompatibility response within Phlox drummondii (Polemoniaceae)
 Dataset DOI: [10.5061/dryad.7m0cfxq73](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](mailto:grace_burgin@fas.harvard.edu),
 [rhopkins@fas.harvard.edu](mailto: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