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bioRxiv · 10.1101/2025.08.27.671803

A Quantitative Polymerase Chain Reaction Protocol for Sex Identification of Zebra Finch and Chicken Using Blood Samples

Subba, P.·Adeniran-Obey, S. O.·Kraft, F.-L. H.·Chapman, S. C.·Shay, N. A.·Liedl, S. R.·Wild, M. D.·Wolcott, S. A.·George, J. M.
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Abstract

Studies of early development in birds typically rely on PCR analysis of genomic DNA to identify embryonic or neonatal sex. In zebra finches and other birds, males are the homogametic sex (ZZ) while females are heterogametic (ZW), and females are distinguished by the presence of specific sequences on the female-specific W chromosome. However, when only a single W locus is analyzed, lack of a PCR product in a sample could potentially arise from genetic variation or technical failure of the amplification, leading to false identification of female samples as males. To mitigate this concern, we developed an approach that targets two different W loci, using SYBR-based quantitative PCR to analyze amplification curves. We applied this method to determine sex of 30 zebra finch embryos (embryonic day 13) and subsequently confirmed genetic sex by brain transcriptome sequencing. We also identified and tested primer sets that are effective for sex determination in chickens.

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Subba, P., Adeniran-Obey, S. O., Kraft, F.-L. H., Chapman, S. C., Shay, N. A., Liedl, S. R., Wild, M. D., Wolcott, S. A., George, J. M.. 2025-08-28. A Quantitative Polymerase Chain Reaction Protocol for Sex Identification of Zebra Finch and Chicken Using Blood Samples. https://doi.org/10.1101/2025.08.27.671803

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