https://doi.org/10.5061/dryad.ns1rn8q13

Using inbred lines of Mimulus guttatus and M. nasutus derived from the sympatric site Catherine Creek (CAC), we produced three Recombinant Inbred Line (RIL) populations from crosses between a common M. nasutus maternal parent CAC9 and the M. guttatus paternal parents CAC110, CAC162, and CAC415. Dataset includes genetic and phenotypic (male and female fertility) data for these RIL individuals.

Description of the data and file structure

Male_Fertility: Raw male fertility data for each RIL individual (Plant) in each RIL population (RIL_pop), including the number of darkly stained (Viable) and unstained (Inviable) pollen grains counted from a haphazardly selected group of ≥100, after staining with lactophenol-aniline blue stain, and the proportion of pollen grains which were viable (PropV). Because each row represents pollen collected from a separate flower, each RIL individual is referenced in multiple rows.

Female_Fertility: Raw female fertility data for each experimental cross made between RIL individuals by pollinating the emasculated maternal parent (M_Parent) with pollen from the paternal parent (P_Parent), including the number of mature seeds produced by each hand pollination (Seeds_per_Fruit) during either of the two growouts (Year). During the 2018 growout multiple fruits of the same cross were collected together, making Seeds_per_Fruit an average over 1 or more fruits, during the 2022 growout each fruit was collected separately, so each row represents the number of seeds contained in a single fruit. As such each cross from 2018 is represented by a single row, while each cross from 2022 is represented by 1 or more rows, depending on the number of hand pollinations performed. Data is also grouped by the RIL population of the maternal and paternal plants (Cross_Group), for example a CAC110 RIL plant pollinated by a CAC162 RIL plant is in cross group 1x2, a CAC162 RIL plant pollinated by a CAC415 RIL plant is in cross group 2x3, etc.

CAC110 RILs QTL Mapping: Files used as inputs for QTL mapping (r/QTL) in CAC110 RILs

• CAC110RILs_Genos_Min_for_rQTL: Genotype matrix used in r/QTL containing genotypes for each CAC110 RIL individual (id) at each 50kb windowed marker (AA: Homozygous M. guttatus alleles, BB: Homozygous M. nasutus alleles, - : Missing data). Markers are named based on the starting position of the window they represent, for example window Chr_01_350000 consists of position 350,000 - 400,000 on chromosome 1. Linkage map information including linkage group number, and map position in cM is included beneath each marker.
• CAC110RILs_PropV_Ave: Average proportion of viable pollen grains across all counted flowers (AvePropV) and the logit transformation of those proportions (LogitAvePropV) for each CAC110 RIL individual (id).
• CAC110RILs_FemaleSter_Ave: Calculated least square means of female fertility (FemaleSter), using seeds per fruit as a proxy, from a linear mixed model including maternal parent genotype (fixed effect), average pollen viability of the paternal parent (fixed effect), a unique RIX identifier nested within RIX cross type (random effect), and the year that the cross was made (random effect), and the square root transformation of those values (SqRootFemaleSter) for each CAC110 RIL individual (id).

CAC162 RILs QTL Mapping: Files used as inputs for QTL mapping (r/QTL) in CAC162 RILs

• CAC162RILs_Genos_Min_for_rQTL: Genotype matrix used in r/QTL containing genotypes for each CAC162 RIL individual (id) at each 50kb windowed marker (AA: Homozygous M. guttatus alleles, BB: Homozygous M. nasutus alleles, - : Missing data). Markers are named based on the starting position of the window they represent. Linkage map information including linkage group number, and map position in cM is included beneath each marker.
• CAC162RILs_PropV_Ave: Average proportion of viable pollen grains across all counted flowers (AvePropV) and the logit transformation of those proportions (LogitAvePropV) for each CAC162 RIL individual (id).
• CAC162RILs_FemaleSter_Ave: Calculated least square means of female fertility (FemaleSter), using seeds per fruit as a proxy, from a linear mixed model including maternal parent genotype (fixed effect), average pollen viability of the paternal parent (fixed effect), a unique RIX identifier nested within RIX cross type (random effect), and the year that the cross was made (random effect), and the square root transformation of those values (SqRootFemaleSter) for each CAC162 RIL individual (id).

CAC415 RILs QTL Mapping: Files used as inputs for QTL mapping (r/QTL) in CAC415 RILs

• CAC415RILs_Genos_Min_for_rQTL: Genotype matrix used in r/QTL containing genotypes for each CAC415 RIL individual (id) at each 50kb windowed marker (AA: Homozygous M. guttatus alleles, BB: Homozygous M. nasutus alleles, - : Missing data). Markers are named based on the starting position of the window they represent. Linkage map information including linkage group number, and map position in cM is included beneath each marker.
• CAC415RILs_PropV_Ave: Average proportion of viable pollen grains across all counted flowers (AvePropV) and the logit transformation of those proportions (LogitAvePropV) for each CAC415 RIL individual (id).
• CAC415RILs_FemaleSter_Ave: Calculated least square means of female fertility (FemaleSter), using seeds per fruit as a proxy, from a linear mixed model including maternal parent genotype (fixed effect), average pollen viability of the paternal parent (fixed effect), a unique RIX identifier nested within RIX cross type (random effect), and the year that the cross was made (random effect), and the square root transformation of those values (SqRootFemaleSter) for each CAC415 RIL individual (id).