Young Sun Hwang^1,2†, Minseok Seo^3,4†, Sang Kyung Kim^1,2, Sohyun Bang³, Heebal Kim^1,2,3, Jae Yong Han^1,2*

¹Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea; ²Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea; ³C&K Genomics, Seoul, Republic of Korea; ⁴Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, United States

The first wave of transcriptional activation occurs after fertilisation in a species-specific pattern. Despite its importance to initial embryonic development, the characteristics of transcription following fertilisation are poorly understood in Aves. Here, we report detailed insights into the onset of genome activation in chickens. We established that two waves of transcriptional activation occurred, one shortly after fertilisation and another at Eyal-Giladi and Kochav Stage V. We found 1544 single nucleotide polymorphisms across 424 transcripts derived from parents that were expressed in offspring during the early embryonic stages. Surprisingly, only the maternal genome was activated in the zygote, and the paternal genome remained silent until the second-wave, regardless of the presence of a paternal pronucleus or supernumerary sperm in the egg. The identified maternal genes involved in cleavage that were replaced by bi-allelic expression. The results demonstrate that only maternal alleles are activated in the chicken zygote upon fertilisation, which could be essential for early embryogenesis and evolutionary outcomes in birds.