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1. Fertilisation rate is closely related to the reproductive performance and economic status of chicken laying breeders. In this study, two flocks ( n  = 1,029 in population I and  n  = 358 in population II) in the later laying period were used for investigating the individual differences among population fertilisation rates (FRs). 2. The funnel and distal parts of the infundibulum were collected from nine individuals (five with low FR and four with high FR from population II) and RNA-sequencing (RNA-seq) method was used to investigate the transcriptome differences in fertilisation. Differences in fertilisation regulation were investigated by comparing the different parts (funnel and distal) of the infundibulum between the low FR and high FR groups. 3. There were notable individual FR differences in both categories. Some individuals had a relative high FR (≥90%) for a long time (&gt;5 days after AI), contrarily, some individuals lost the ability to fertilise eggs in a very short time. 4. Differentially expressed genes (DEGs), such as  DUSP7 ,  PPP1R3B ,  FYB, OVA ,  OVALX and OVALY  may be associated with sperm functional regulation, fertilisation and early-stage fertilised ovum development processes. DEGs such as  AVBD1, AVBD2, AVBD6, NFATC2  and  BANK1  indicated a severe immune response to sperm survival and fertilisation in the oviduct. 5. The results suggested that individual differences should be considered in the breeding and reproduction process. The DEGs identified in this study may promote our understanding of different fertilisation regulation in laying breeders.

Transcriptome analysis and identification of genes associated with individual fertilisation rate differences in hen infundibulum