Why not just do a visual determination by examining the embryo disk? In eggs of similar age, you can quite easily see the difference between fertile (very round, slightly donut-shaped embryo disk, sometimes with a white dot in the middle) compared to infertile (more intensely white, but irregularly shaped) embryo disk. If you are unsure, start by comparing some known samples. The method becomes more difficult after eggs are stored too long. The back-up, more labour intensive method is to do the perivitelline sperm penetration assay. It shows how many sperm have gotten through the perivitelline layers deposited over the yolk (and site of fertilization) just after ovulation. This can be used to assess POTENTIAL fertility on a flock basis if the yes/no answer from the visual determination of fertility described above is not what you are looking for. I believe we show the differences in a chapter of one of the books I was involved with. I can send you the chapter if you like.
I work with double-yolked eggs and it was suggested in some papers that the first yolk passing down in the oviduct is more likely to be fertile (if they are not ovulated simultaneously), as the majority of sperm is released from the secondary sperm storage sites. Further the sperm in transit in the oviduct gets trapped in the albumen secreted around the first yolk, therefore the second yolk has a smaller chance of being fertilized (see Salamon and Kent, in press in Reproduction Fertility and Development). However so far I could not find any papers that identified trapped sperm in the albumen in double-yolked eggs.
But I would appreciate if you could send me the chapter of that book dealing with the perivitelline sperm penetration assay.
My understanding is that in commercial chicken, the sperm storage tubules at the base of the infundibulum are basically empty. The tubules at the utero-vaginal junction are the ones that matter the most. This may differ in the birds you are looking at. Because the sperm are traveling up the oviduct at the base of the folds in the oviduct surface, they are not simply being washed out as the egg/yolk passes. The question you have comes down to the impact of the newly ovulated yolk passing by on sperm movement upstream. While fertility is lower in the hour or so just before and after the egg is laid, I'm less clear on if just the yolk passing is enough to negatively affect sperm travel.
What the aim of your study to detect , for example produce two chicks from double-yolk egg or to improve the fertility in flock produce many double-yolk egg.
The double-yolk egg usually sorted as abnormal egg and not included in hatchery now.
The early studies recorded low fertility in this type of egg ( 42.9%) and 27% contained two embryos, beside that single and double embryos died at different stages of development.
In other hand, there were cases for hatching two chicks from one egg , please use the links:
I wrote my PhD mainly about double yolked eggs. As part of it I studied the fertility of double yolked eggs and I found that the fertility of one of the yolks is generally higher. I think the yolk that has a higher chance of fertilization is the first to pass down the oviduct and the one that passes down second has lower chance of fertilization, because the sperm can get caught in the albumen surrounding the first yolk. However, I got some help and I will look the sperm hole distribution over the germinal discs of both yolks in double yolked eggs.