microsatellite analysis (Animalia)

Knowledge graph centered on microsatellite analysis (Animalia) with 75 nodes and 179 connections. Top connected: Marmota flaviventris, Ligusticum porteri, Spruce, Bacteria, Arabidopsis.

Method synopsis

Pooled whole genome sequencing approach using DNA from multiple individuals per population to identify SNPs associated with environmental variables and population differentiation patterns.

Synthesized from method descriptions across 4 papers 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 — Evolution and genomic basis of the plant penetrating ovipositor: a key morphological trait in herbivorous Drosophilidae (2022), Proceedings of the Royal Society B. The protocol was originally introduced by Microsatellite-based species identification method for <i>Drosophila virilis</i> group species (2007), Hereditas. Implementations in other papers (listed below) may differ.

1. Establish laboratory populations
   Two S. flava outbred laboratory populations were founded from collections on mustard plants, one larvae per plant, in Portsmouth, NH, USA. One population (NH1) was founded from 79 larvae and the second (NH2) from 58 larvae from T. glabra and Barbarea vulgaris. Within each population, newly eclosed flies were transferred to one mesh cage containing Arabidopsis thaliana (Col-0 accession) and allowed to mate randomly.
   Quantities: NH1: 79 larvae founding population; NH2: 58 larvae founding population; Over 1200 offspring (G1) were generated on a mixture of T. glabra, B. fridgidaDuration: Multiple generations maintainedConditions: Laboratory conditions with controlled mating on host plants
   Equipment: mesh cages, Arabidopsis thaliana plants, T. glabra, Barbarea vulgaris, B. fridgida
2. Create extreme phenotype pools
   Flies were split into phenotypically extreme pools per population (four pools: NH1-low, NH2-low, NH1-high, NH2-high), composed of 60-85 females in the upper or lower 20% tail of the distribution of residual bristle number. Residual bristle number was determined through a linear regression of ovipositor bristle number against ovipositor length using the lm function in R.
   Quantities: 4 pools total, 60-85 females per pool, upper or lower 20% of distributionDuration: Not specifiedConditions: Laboratory selection based on statistical distribution

Typical Equipment

• collection containers
• ethanol
• CTAB solution
• Qubit
• Illumina HiSeq3000
• FASTQC
• TRIMMOMATIC
• BWA-MEM
• SAMTOOLS
• GATK

Output Measurements

• SNP frequencies
• FST values
• population genetic statistics

Papers Using This Protocol (4)

Species Studied With This Protocol