Bird Sexing PCR Protocol – CHD1F/CHD1R primers


This protocol allows you to test for the sex of a bird by amplifying a region of the CHD1-Z and CHD1-W genes on the Z and W sex chromosomes, using plucked feathers as a DNA source.

The CHD1F/CHD1R primer set was designed by Lee et al. (2010) based on the 2550F/2718R primer set of Fridolfsson & Ellegren (1999), to produce smaller amplicons that would be more suitable for capillary electrophoresis analysis and when working with more degraded DNA. A consequence of using different primer sequences is that the CHD1F/CHD1R primer set is able to sex some bird species more successfully than 2550F/2718R (see Çakmak et al., 2017).

However, as a more recently developed bird sexing primer set, CHD1F/CHD1R has been used much less in published studies than either P2/P8 and 2550F/2718R, and there are fewer examples of it being used successfully with specific bird species than with the other two primer pairs.

This protocol is specific to the CHD1F/CHD1R primer set. These primers will enable you to sex a range of birds including landfowl, pelicans, flamingos, birds of prey, waterfowl and songbirds.


Çakmak, E., Akın Pekşen, Ç., & Bilgin, C. C. (2017). Comparison of three different primer sets for sexing birds. Journal of Veterinary Diagnostic Investigation29(1), 59-63.

Fridolfsson & Ellegren (1999). A simple and universal method for molecular sexing of non-ratite birds. Journal of avian biology, 116-121.

Lee et al. (2010). A novel strategy for avian species and gender identification using the CHD gene. Molecular and cellular probes24(1), 27-31.


To start this protocol you need to have extracted DNA from your feather samples, using either the DNA Extraction from Feathers – HotSHOT Kit protocol or a comparable DNA extraction method.

Directly before PCR, you should have prepared 1 in 10 dilutions of your DNA extractions in PCR grade water, as described in the protocol above.

  1. PCR

    You will need your DNA extractions (1), an empty PCR tube (2), an empty 1.5 mL microcentrifuge tube, the primer mix for this project (3), Firepol master mix (4), and PCR grade water (5).

    The first step is to calculate how much PCR reaction mix you require for your samples.

    PCR reaction mix is the combination of Firepol master mix, primer mix and PCR grade water you will add to each PCR tube before adding your DNA extraction.

    For each sample, you will need:

    • 4 µL of Firepol master mix
    • 10 µL of PCR grade water
    • 2 µL of primer mix
    • 4 µL of DNA template

    You also need a negative control.

    A negative control is a PCR tube of PCR reaction mix that you do not add DNA to. This is used to check your PCR reaction mix is not contaminated.

    If you are doing multiple reactions using the same primers, you can first make a reaction mix containing all of the shared reagents. This means less pipetting, and you will use less pipette tips.

    To calculate how much of each reagents you will need:

    [number of DNA extractions] + [negative control] + 10%

    For example, if you have 9 samples from your DNA extractions:

    9 DNA extractions + 1 negative control + 10% = 11 repeats of PCR reagents

    • 11 x 4 µL = 44 µL of Firepol master mix
    • 11 x 10 µL = 110 µL of PCR grade water
    • 11 x 2 µL = 22 µL of primer mix

    In this example, you would use the 20-200 µL adjustable pipette to transfer the 44 µL of Firepol master mix, 110 µL of PCR grade water and 22 µL of primer mix into a 1.5 mL microcentrifuge tube. Make sure to use a fresh pipette tip each time.

    Close the lid of the 1.5 mL microcentrifuge tube and invert several times to ensure thorough mixing of your PCR reaction mix.

    If you are using a PCR reaction mix, set the 2-20 µL adjustable pipette to 16 µL and transfer 16 µL of PCR reaction mix into the required number of PCR tubes.

    If you are not using a PCR reaction mix, use a 2-20 µL adjustable pipette to add each item (4 µL of Firepol master mix, 10 µL of PCR grade water and 2 µL of primer mix) individually to the PCR tube.

    Use a permanent marker to label the PCR tubes with your sample names. Label the negative control too so you know not to add DNA to this PCR tube.

    Now add the DNA extraction. Set your micropipette to 4 μL.

    Using a fresh pipette tip, transfer 4 μL of your DNA extraction into the correspondingly labelled PCR tube containing PCR reaction mix. Then discard your tip.

    Make sure to keep your DNA extraction upright and pipette from the surface of the liquid.

    The DNA extractions contain PCR inhibitors that will prevent your PCR from being successful if the liquid is mixed.

    When you have pipetted the DNA extraction into the PCR tube, close the lid and invert the tube several times to ensure the DNA is mixed into the PCR reaction mix.

    Tap the PCR tube firmly on a hard surface to collect the liquid at the bottom and to ensure there are no air bubbles in the liquid.

    Place your PCR tubes in the thermocycler block.

    Set up the thermocycler with the following PCR program:

    CHD1F/CHD1R primers

    • 4 mins at 94°C (or 15 mins at 94°C if using 5x HOT FIREPol® Blend Master Mix Ready to Load)
    • 8 cycles made of 3 steps:
      • 30 sec at 94°C
      • 45 sec at 57-50°C (touchdown)
      • 45 sec at 72°C
    • 27 cycles made of 3 steps
      • 30 sec at 94°C
      • 45 sec at 50°C
      • 45 sec at 72°C
    • 5 mins at 72°C
    • ∞ at 15°C

    (For help setting up a touchdown PCR on your Bento Lab visit the PCR Thermocycler User Manual.)

    If you need help operating the Bento Lab thermocycler, check the manual. You can use the PCR  preset (1), then modify (2) the program to the required settings (3) before running the program (4).

    The program will run for ca 2 hours. When it is finished, you can keep the result in the freezer, or use it right away for gel electrophoresis.

  2. Gel Electrophoresis

    Follow the Gel Electrophoresis Protocol to pour a gel and run it with your PCR results, negative control and a 100bp ladder.

    For this protocol you will need to pour a 3% gel (2 agarose tablets in 33 mL of 0.5X TBE) with a single gel comb, load your samples, and run the gel at 50V for 1.5 hours.

    You can visualise the gel after ~15 minutes to check for the presence of bands. Running for 1.5 hours will allow bands to separate so you can determine gender.

  3. Visualising the Gel

    After the gel run has completed, you can visualise your results.

    Continue to wear gloves as you handle the gel.

    Open the orange lid of the gel box, and wipe off the condensation.  

    Gently pour out the buffer, and dispose of the buffer down a drain.

    Drain disposal of TBE running buffers is a standard waste disposal procedure followed by research labs. If you have questions, get in touch with us.

    Place the gel box onto the Bento Lab transilluminator surface. In order to get best visibility, you should do this in a room as dark as possible.

    Turn Bento Lab on, select the Gel Electrophoresis module, and turn on the Transilluminator light.

    Hold the orange filter lid over the gel to visualise the DNA bands. For documentation, use your mobile phone to take a clear picture of the gel. Rather than holding the lid over the gel, you can hold the lid directly in front of your camera lense.

    If the bands are faint, try to reduce the light in the room, e.g. by closing the curtains and turning off the lights.  You can also carefully take the gel out of the gel box and place it directly onto the transilluminator. Wear gloves when doing this, and be careful not to break the gel.

  4. Analysing your results

    Compare the picture of your gel to this example result, which has been run with all variations. Your sample should correspond to one of these variations.

    Avian Sexing PCR Model Result for CHD1F/CHD1R primers. Female bands at 700bp and 500bp, Male bands at 500bp

    1 – Ladder – 100 bp DNA Ladder

    2 – Female chicken DNA using CHD1F/CHD1R primers – two distinct bands: one at ~320bp and one at ~500bp.

    3 – Male chicken DNA using CHD1F/CHD1R primers – one band at ~500bp.

    4 – Negative control – there should not be any bands in this lane. If there are, it is likely that your PCR reaction mix was contaminated and you need to repeat the PCR.

    Your results – two bands indicate DNA is from a female bird and one band indicates DNA is from a male bird.

    Do not worry if the bands from your samples are different sizes to the chicken DNA. Band sizes vary depending on the species of bird you have extracted DNA from.

    After you have taken good photos of the gel for your documentation, you can dispose of the gel in your regular bin.

    Disposal of agarose gels is a standard waste disposal procedure followed by research labs. If you have questions, get in touch with us.

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