SDR haplotype genotyping in wild strawberry (Rosaceae)

Knowledge graph centered on SDR haplotype genotyping in wild strawberry (Rosaceae) with 21 nodes and 58 connections. Top connected: climate change effects on species interactions, space use, Silene, Fragaria, Fragaria virginiana.

Method synopsis

PCR-based genotyping to identify sex chromosome haplotypes in the sex-determining region (SDR) of Fragaria virginiana, distinguishing between alpha, beta, and gamma variants.

Synthesized from method descriptions across 1 paper using this protocol.

Procedure from a recent peer-reviewed implementation

Steps below were extracted from the most recent peer-reviewed implementation of this protocol in the corpus — Range-wide study in a sexually polymorphic wild strawberry reveals climatic and soil associations of sex ratio, sexual dimorphism and sex chromosomes (2025), Journal of Ecology. Implementations in other papers (listed below) may differ.

1. Collect leaf samples for genetic analysis
   Selected 298 specimens collected between 1950 and 2022 from herbarium records containing flowering female F. virginiana and received leaflet samples from hosting herbaria. Also collected leaf tissue from 47 female F. virginiana maintained by USDA ARS National Clonal Germplasm Repository in Corvallis, Oregon. Additionally included 21 female plants with SDR determination from Tennessen et al. (2018).
   Quantities: 298 herbarium specimens plus 47 germplasm accessions plus 21 previously studied plants = 366 total samples for genetic analysisDuration: Specimens collected 1950-2022Conditions: Preserved leaf tissue suitable for DNA extraction
   Equipment: USDA ARS National Clonal Germplasm Repository samples
2. Extract DNA and perform SDR genotyping
   Extracted DNA from 0.5 cm² of leaf tissue using Ag-Biotech Inc. (Monterey CA) protocol. Designed primers to determine presence of female-specific sex-determining region (SDR) and differentiate three SDR haplotypes (alpha, beta, gamma). Used PCR assays with Primer3 and Geneious 9.1.8 software to amplify and genotype samples. Performed presence/absence PCR and differentiation PCR to classify haplotypes.
   Quantities: 0.5 cm² leaf tissue per sample, multiple PCR assays per sampleDuration: Not specifiedConditions: Laboratory DNA extraction and PCR conditions
   Equipment: Ag-Biotech Inc. DNA extraction kit, Primer3 software, Geneious 9.1.8, PCR equipment

Typical Equipment

• Ag-Biotech Inc. DNA extraction kit
• Primer3 software
• Geneious 9.1.8
• PCR equipment

Output Measurements

• SDR haplotype
• sex chromosome type

Papers Using This Protocol (1)

Species Studied With This Protocol