There are two very distinct possibilities as to why milk fat levels are varied like they are. The elephant in the room to both is management: Feeding management, or milking management.
Diet affects milk fat levels by way of the amount of forage or long-stemmed roughage (such as hay) is being fed to the cow, compared with readily fermentable carbohydrates (RFCs) like grain or other concentrates. The more concentrate a cow gets, the less milk fat she can produce. The opposite is true with long-stemmed forages, like hay or baleage.
Long-stemmed forage tends to increase certain volatile fatty acids (VFAs) produced in the rumen, namely acetate and butyrate. These two VFAs are associated with increased milk fat. The third VFA that is less associated with forage is propionate. Propionate levels tend to increase when more starch or RFCs are fed. Propionate is associated with lower levels of milk fat.
There's what's called an "acetate-to-propionate ratio" that determines milk fat levels in dairy cows. Basically, the higher the acetate:propionate ratio, the greater the milk fat content. Conversely, the lower the acetate:propionate ratio, the lower the milk fat content.
Thus, the possible scenario could be that the cow is being limit-fed hay during a certain time of the day, such as an hour or so after the morning milking. This could influence high milk fat levels seen in the evening. However if hay ran out overnight and the cows had to wait until after milking to next feeding, this could be a cause for the lower milk fat levels in the morning.
Another possibility is that the cows are being fed two different feeds at two different times, both after milking: Hay in the morning after milking, then some concentrate or silage in the evening after the evening milking; these could possibly cause the different milk fat contents noticed at the two different milkings.
If feeding management is the main culprit here, then obviously there needs to be more consistency with feeding cows: Make sure they have plenty of hay, and feed free-choice instead of limited access where they're more at risk to run out overnight. If feeding twice a day, keep both feedings consistent and with the same ingredients at each feeding, not hay in the morning then silage in the evening type of deal. These practices will help keep milk fat levels a bit more even during the two milkings.
But, what if feeding management is not the culprit? Then it's time to turn our attention to milking management.
The primary reason that milk fat levels are low in the morning and high at night, with respect to milking management, is that the cows are not being completely milked out.
Milk fat content tends to increase continuously through the milking process. The lowest fat milk is drawn first, and the highest fat milk is drawn out last. This is because of the fat globules in the mammary alveoli tend to get clustered up and trapped, making themselves as the hardest compounds to move down from the alveoli into the ducts and milk canals of the mammary tissues compared with other milk compounds.
Thus, if the cows are not completely milked out in the morning, the person asking this question will get milk with fat content that is lower than normal for that morning milking. Then, at the next milking during the evening, the milk fat content will be abnormally higher than normal.
Source: J.G. Linn. 1988. Factors Affecting the Composition of Milk from Dairy Cows.
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